In order to promote the trading and accelerate the transformation of agricultural scientific and technological achievements (ASTA), a WebGIS-based system for evaluating the value of ASTA was designed and developed. Object-oriented JAVA language was adopted to realize various functions of the system. The functions included the storage and management of spatial and temporal data, value evaluation of ASTA, spatial and temporal characteristics analysis of value evaluation results and visualization of the results. As an integrative tool for managing data and analyzing spatial and temporal characteristics, the system provided service for agricultural scientific and technological achievements management department. Comprehensive fuzzy method was adopted to evaluate the value of ASTA. In order to ensure the accuracy of evaluation results, the indexes were extracted from many influence factors and then the evaluation index system was constructed. The index system took into account all the influence of technology, market and benefit. So far, totally 265 ASTA were evaluated in the system, which were produced in 2010—2015. To validate the correctness of the system, an experiment was carried out, and results showed that the accuracy of the system was good. The application of the system showed that it provided an efficient-fast third-party assessment tool for ASTA holders, and it also supplied an intelligent management tool for ASTA management department. Furthermore, evaluation results of the system can provide reference for ASTA trading.