To investigate the characteristics of Tsongkhapa’s meditation thought, the study is divided into five parts: (1) introduction, (2) Tsongkhapa’s exposition of meditation practice, (3) the Madhyamaka thought in Tsongkhapa’s vipassanā, (4) the characteristics of Tsongkhapa’s meditation thought, and (5) conclusion. Generally perceiving śūnyatā as nonexistence after death, scholars in Tsongkhapa’s time have denied the importance of intellectual thinking and completely negated the significance of ethics and precepts, and this has greatly endangered Tibetan Buddhism. In order to remedy this situation, Tsongkhapa combines Nagarjun’s Madhyamaka insight and Maitreya and Asaṅga’s universal practice and develops the meditation thought, a practice system featuring order and steady progress. An outstanding part in Tsongkhapa’s meditation thought is the Madhyamaka thought in the chapter of vipassanā, and this study analyzes it with five points: (1) differentiation between nītārtha and neyārtha, (2) pratītyasamutpāda and śūnya, (3) differences between the Prāsaṅgika and the Svātantrika, (4) criticism of the Free from Extremes Madhyamaka, and (5) choice between pudgala-anātman and dharma-anātman. This study brings out the features of Tsongkhapa’s meditation thought as follows: (1) correction on the mistakes of Han and Tibetan worthy predecessors and illustration of the Right View in Madhyamaka thought, (2) strict compliance with the sequence of religious practice, (3) the connection between pratītyasamutpāda and śūnya and their development, (4) integration of Madhyamaka insight and universal practice, and (5) meditation practice as preparation for Esoteric Buddhism. Tsongkhapa’s meditation thought has disproved Tibet’s interpretation on śūnyatā, reversed the degeneration of Tibetan Buddhism, and established the perfect sequence of practice that highlights religious discipline, practice sequence, application of both samatha and vipassanā, and compatibility of Exoteric Buddhism and Esoteric Buddhism. Even now, its influences still remain.