Abstract: Efficiency involving in the resource allocation and utilization of the public institutions for agricultural research in Fujian was evaluated. The input-output indices on 22 local science and technology establishments for the years between 2011 and 2015 were analyzed using the DEA-Malmquist method. As a result, the overall TPFC was found to decline approximately 7.1% annually. Although TEC slightly increased, but the substantial decrease in TC resulted in the downward trend of TPFC at 68.18% of the organizations. Based on the evaluation, the institutions were grouped into low-efficiency, in-between, low-growth, and high-growth categories, and approaches for improvement were formulated for consideration.