Data enveloping analysis is a quantitative analysis method developed on the basis of the concept of “relative efficiency evaluation”, which has outstanding advantages in solving the relative efficiency evaluation of DMU with multiple input and multiple output indexes. Technological innovation is the driving force for enterprises to obtain competitive advantages and an important guarantee for sustainable development of enterprises. This paper constructs an enterprise technological innovation evaluation system based on data envelopment analysis to assist enterprises to carry out technological innovation evaluation and improve the scientific level of enterprise technological innovation decision-making. Firstly, the mathematical model of data enveloping analysis is constructed, including classical CCR model and BCC model, and the specific application of the model is explained. Then, the evaluation process of DEA model is designed to lay a foundation for the program development. Then, the functional framework of the system is designed, which is composed of system example construction and evaluation sample data input. Finally, an empirical study is carried out on the technological innovation data of 23 enterprises to verify the data envelopment analysis model and test the system. The test results show that the system is reliable and the model is applicable.