Under the background of the current information age, the electronic and intelligent transformation of the bidding industry has become an inevitable trend, and the e-bidding model stands out and greatly improves people’s understanding of bidding. Aiming at the traditional e-bidding system, in order to solve the problem of the lack of the traditional e-bidding system that provides the bidding body with referable opinions, this study firstly constructs the e-bidding risk assessment indexes and realizes the optimization of the evaluation module of the system. Then the recommendation algorithm based on deep learning implements the optimization design of the e-header bidding system. This study constructs an optimized recommendation model by fusing knowledge graphs on the basis of deep learning. Then the e-tendering optimization system is designed according to the actual needs of e-tendering, combined with the recommendation model of this paper. The accuracy index ACC of this paper’s recommendation model is improved by about 3% on average compared with other best-performing recommendation models on each dataset, which verifies the excellent performance of this paper’s recommendation algorithm. This study constructs an optimized e-tendering system and proposes suggestions for the development and operation strategy of corporate e-tendering, contributing to the development of e-tendering transactions and the participation of social capital.