This article explores systematically Master Yin-shun’s Buddhist research in the context of modern Chinese academic history, and analyzes his achievements, especially his complex investigations between scripture studies and historical exploration. The discussion elaborated in this article falls into five parts. The first part investigates the evolution of Buddhist studies in modern China, especially the rise and development of modern Buddhist historiography on the pattern of modern intellectual history, which illuminates a modern intellectual transformation of Buddhist scripture studies and historiography. The second part analyzes how scripture studies were converted into historiography in Yin-shun’s Buddhist research which had tended to use the methods of modern intellectual history. Yin-shun’s research methods of Buddhist historiography such as searching for the origin of Buddhism, as well as the concept of intellectual knowledge, are dealt with in this part. The next part is concerned with the international perspective in Yin-shun’s research on Buddhist historiography, focusing on the influence from Japanese Buddhist studies, which apply the discipline of modern intellectual history. The following part explores Yin-shun’s methods of Buddhist exegesis, analyzing how he mediated and integrated conflicting sources between scripture studies and historiography when he was writing an exegesis, and discussing the difference between the traditional approach of Buddhist exegesis and his method of scriptural interpretation. The last part inspects Yin-shun’s dilemma while integrating knowledge with values, by examining his statement in Buddhist scripture studies and historiography, and modern historical theory as well. The inherent tension in Yin-shun’s thought is also discussed in detail.