This paper discusses Master Yin Shun's methodology in three aspects, i.e. the manner he approaches Buddhism, the way he explores the Middle Way, and the measure he takes to distinguish between the “two truths”. Through these aspects, Master Yin Shun demonstrates that the method and attitude in learning Buddhism is not to take the Buddhist doctrine as any worldly knowledge. The right way for scholars to master Buddhism is based on the “three universal characteristics of Buddha Dharma”; that is to say, the approach by which scholars understand Buddhism should be grounded on an awareness that all existence and phenomena are in a constant state of fluctuation over time and adaptable to space. Only by transcending time-space limits can they grasp Buddhism as a whole and surpass sectarian premises before attaining eternally serene state of Nirvana. In quest of doctrinal clarification of the Middle Way, Master Yin Shun maintains however that the methods collecting worldly knowledge are essential. These methods include “justification of the Middle Way” and “analysis of the Middle Way.” For the method of justification, he approves the concept of Prāsangika-Mādhyamika Buddhism from the thinking of Dependent Origination. As for the method of analysis, he believes that liberation cannot be perceived by separating from worldly nominalities, but it should be reached by cultivating perfect wisdom through valid cognition, inference and perception. This idea approximates to the conception “conformable to ultimate” of Svātantrika School. As regards distinction between the “two truths” or the “four-fold two truths,” Master Yin Shun applies the methods of “horizontal” (relative) and “upright” (absolute) from the Three Sastra Sect, to differentiate “worldly truth” (relative existence) from “ultimate truth” (truth of emptiness), so that Buddha’s core teachings about two truths will be aptly conceived.