This paper first uses Topsis method to measure the innovation of agricultural research institutions from 31 provinces between 1998 and 2011 and then predicts the short-term and long-term dynamic relationships between finance R&D input and innovation of agricultural research institutions.The empirical result shows that long-term elasticity of finance R&D input on innovation of agricultural research institutions is 0.67,and short-term elasticity is 0.55.When deviating from long-term equilibrium,short-term innovation will be adjusted to equilibrium state at a speed of 42.7% by error correction.This paper also verifies the cause and effect relations between finance R&D input and innovation of agricultural research institutions.That is to say,increasing government investment in S&T can promote the innovation of agricultural research institutions,and agricultural research institutions with higher innovation levels can obtain more finance R&D input.In the short term,innovation of agricultural research institutions only has a weak and positive impact on growth in fiscal R&D input,with a contribution of only 2.7%,while the latter applies a significant positive impact on the former one,with a contribution of 47.8%.And there are visible differences in the contributions of eastern,central and western regions.Due to the little contribution of innovation of agricultural research institutions to finance expenditure in science and technology,the gap is quite narrow among provinces with high innovation level and ones with lower levels.It is evident that this situation is not conducive to encouraging innovation of provincial agricultural research institutions.Therefore,it is essential to develop a new mechanism that high innovation level attracts high finance R&D input,which will greatly stimulate innovation enthusiasm of agro-research institutions.