Agriculture and forestry universities is the source of China's agricultural economic development and innovation. The difference of the allocation structure of agricultural and forestry universities will affect the allocation efficiency, which plays an important role in the process of agricultural modernization construction. Based on the analysis of the current input and output structure of agricultural and forestry universities, the system dynamics model of science and technology resource allocation structure of agricultural and forestry universities was constructed using the data of agricultural and forestry universities from 2004 to 2014. By changing the fund appropriation structure and talent distribution structure, the paper simulates the change of output under various programs. Based on this, the paper discusses how to adjust the allocation structure of science and technology resources in agriculture and forestry universities to achieve the optimal output. Hope to provide the basis for related departments to formulate policies.