From the perspective of institutional changes, the impact of fiscal decentralization reform on the flow of agricultural elements and its structural change has been analyzed and the provincial panel data from 1994 to 2017 have been utilized for empirical test. The study shows that the proportions of agricultural labor and land elements in China have declined and the agricultural capital deepening has continuously increased since the reform of tax distribution system. At the regional level, the agricultural capital is relatively abundant in eastern China while the agricultural labor and land elements are relatively sufficient in the central and western areas and their capital accumulation is gaining momentum. Fiscal decentralization has a profound institutional impact on the deepening of China’s agricultural capital. On the one hand, fiscal decentralization promotes the accumulation of agricultural capital by promoting fiscal expenditure on agriculture and industrialization. On the other hand, fiscal decentralization restrains the accumulation of agricultural labor and land elements through accelerating industrialization and urbanization, thus making the agricultural economic growth show a trend of capital-deepening through land saving and labor saving. With the advancing of the fiscal decentralization reform, the above-mentioned effects are constantly reinforced, and exert more influence on the central and western China than on the eastern area.