He hailed from Yongjia 永嘉 in the prefecture of Wenzhou 溫州 (modern Wenzhou, Zhejiang), and is therefore called the founder of the Yongjia School 永嘉學派 of Neo-Confucianism. He obtained his jinshi degree in 1178 and was prefectural judge (jiedu tuiguan 節度推官) of Pingjiang 平江, prefect (zhizhou 知州) of Qizhou 蘄州, Vice Minister of Personnel (libu shilang 吏部侍郎), erudite in the office of the Chamberlain for Ceremonials (taichang boshi 太常博士), prefect of Jiankang 建康 (today's Nanjing) and concurrently *Commissioner-in-chief of the Yangtze patrol (yanjiang zhizhishi 沿江制置使), then academician-in-waiting (daizhi 待制) of the Baowen Hall 寶文閣 and concurrently military commissioner (zhizhishi 制置使), Director of Studies in the Directorate of Education (guozi siye 國子司業) and academician (xueshi 學士) of the Xianmo Bureau 顯謨館.
During the reign of Emperor Ningzong 宋寧宗 (r. 1194-1224), during the prohibition of court factions of the Qingyuan reign-period (1195-1200, Qingyuan dangjin 慶元黨禁), he defended the philosopher Zhu Xi 朱熹 (1130-1200) against slandering at the court, and was therefore registered as a "factionalist" and member of the "heretic scholar faction" (weixuedang 偽學黨) and lost his office. As a politician, Ye Shi advocated a war of reconquest of northern China that was occupied by the Jurchen empire of Jin 金 (1115-1234). When Counsellor-in-chief Han Tuozhou 韓侂胄 (1152-1207) undertook a badly organized campaign against the Jurchens, Ye Shi was ordered to take over command of the city defence of Jiankang 建康 (modern Nanjing 南京, Jiangsu), and when the Jin armies attacked the city across the Yangtze River, Ye Shi successfully routed them and so contributed to the survival of the Song dynasty. In 1208 Han Tuozhou was executed as a traitor, and Ye Shi again lost his office as a collaborator of Han. Ye returned to his home district and became a private teacher.
Ye Shi was a disciple of Xue Jixuan 薛季宣 (1134-1173) and Chen Fuliang 陳傅良 (1137-1203) and expanded the philosophical theories of these two masters. He became so important that he was seen as the most important Southern Song philosophers, apart from Zhu Xi and Lu Jiuyuan 陸九淵 (1139-1193). His approach to philosophy was a very practical one because of his own experience in administrative affairs. Righteousness (yi 義), therefore, could not be separated from "profit" (li 利), while the traditional Confucians despised profit. Ye Shi explained that if cultivation did not result in yields (li), any righteousness of the Confucian Way would be meaningless. His aim was therefore to reconcile profit with the altruistic principle of righteousness (yi li he yi, bu yi yi yi li 以利和義，不以義抑利 "reconcile profit with righteousness, do not suppress profit for righteousness"). When extending this ideal to the realm of society, it should be possible to look beyond the narrow paradigm of "esteeming agriculture and suppressing commerce" (zhong nong yi shang 重農抑商), and to incorporate commerce and artisanry into social concepts, and to make business profitable for state and the whole society.
In contrast to this seemingly modern conception, Ye Shi also operated with the traditional theory of the Five Agents (wuxing 五行) and the Eight Trigrams (bagua 八卦) that were very popular in Neo-Confucianism. It was believed that with the help of these about a dozen of symbols it was possible to describe the whole universe. All objects in the universe consisted of substance (qi 氣) that was more or less condensed, and so constituted that matter of which things were made. Ye Shi explained that in all objects, the natural principle or "Way" was to be found: Dao bu li qi 道不離器 "The Way does not leave the implements/objects." Following Daoist belief he explained that on the one hand, the Way was as large as the universe itself (i.e. endless), but on the other hand so small that it could be found in all objects. It was possible to perceive the Way by the sensory organs that guided perceptions into heart and mind. Any cognition was so seen as a reflectance of the outer world, and must therefore be seen as objective.
Ye Shi studied the early history of Confucianism and came to the conclusion that it was not correct to assume a direct decendency from Confucius' teachings to Meng Ke 孟軻 (385-304 or 372-289 BCE, Mengzi 孟子) by way of transmission through Confucius' disciple Zeng Shen 曾參 (505-436, Zengzi 曾子) and Zeng Shen's disciple 孔伋 (483-402 BCE, Zisi 子思). This finding proves that Ye's approach to use historiographic sources for the interpretation of Confucian writings was very important and creative. He can therefore be seen as a forerunner of the Qing-period 清 (1644-1911) scholar Zhang Xuecheng 章學誠 (1738-1801), who explained that the Six Classics (liujing 六經) were in fact all historiographical writings.
The most important, surviving writings of Ye Shi are the collections Shuixin wenji 水心文集 and Shuixin bieji 水心別集, as well as his book Xuexi jiyan xumu 習學紀言序目.