Based on the data from the 1991–2016 agricultural investment of China's Taiwan in China's Mainland and the agricultural GDP of the latter, through models of vector autoregressive (VAR) and vector error correction (VEC), the influences of China's Taiwan agricultural investment on the development of agriculture in the eastern, central, and western regions of China are discussed. The results show a long-term equilibrium relationship between China's Taiwan agricultural investment and agricultural development in China's eastern, central, and western regions. In the long term, China's Taiwan investment in agriculture in the eastern, central, and western regions of China have certain positive promoting effect on their agricultural development. However, there is an obvious regional diversity in investment effect: Impulse response and variance decomposition show that the positive effect from China's Taiwan agricultural investment in China's western region agricultural development is most significant, and it is significantly higher than that in the eastern region; its contribution to the central region's agricultural development is little. VEC model analysis shows that in the short term, China's Taiwan investment in agriculture has a significant positive effect on the agricultural development of China's eastern region, but not on the agricultural development of the central and western regions.