The body of agricultural research consists of agricultural universities and research institutes from the perspective of the Public Goods Theory.Based on the Almon PDL model,this paper gave an estimation to the hysteresis effect of R&D inputs into outputs and measured the agricultural university scientific research effectiveness index by using Malmquist-DEA and BCC-DEA method.It has been found that the agricultural university scientific research effectiveness index showed a decline tendency,there’s no discrepancy overall between the "985 program" and "211 program" universities but significantly higher output for the later lonsidering the effectiveness of furding.It finally pointed out that based on the effectiveness evaluation,higher education should change development priority of the fiscal appropriation,the scientific research funding allocations should take a prudent growth pattern.