This study aims to speed up the progress of scientific research projects in colleges and universities, continuously improve the innovation ability of scientific research teams in colleges and universities, and optimize the current management methods of performance appraisal of college innovation ability. Firstly, the needs of the innovation performance evaluation system are analyzed, and the corresponding innovation performance evaluation index system of scientific research team is constructed. Secondly, the Internet of Things (IoT) combines the Field Programmable Gate Array (FPGA) to build an innovation capability performance appraisal management terminal. Thirdly, the lightweight deep network has been built into the innovation ability performance assessment management network of university scientific research teams, which relates to the innovation performance assessment index system of scientific research teams. Finally, the system performance is tested. The results show that the proposed method has different degrees of compression for MobileNet, which can significantly reduce the network computation and retain the original recognition ability. Models whose Floating-Point Operations (FLOPs) are reduced by 70% to 90% have 3.6 to 14.3 times fewer parameters. Under different pruning rates, the proposed model has higher model compression rate and recognition accuracy than other models. The results also show that the output of the results is closely related to the interests of the research team. The academic influence score of Team 1 is 0.17, which is the highest among the six groups in this experimental study, indicating that Team 1 has the most significant academic influence. These results provide certain data support and method reference for evaluating the innovation ability of scientific research teams in colleges and universities and contribute to the comprehensive development of efficient scientific research teams.