Since the energy consumption of joint processing in uplink multi-base cooperative communication system is excessively high, an Inter-Cell Interference Rejection based Uplink Multi-Base Cooperative Energy Efficiency Algorithm (ICIR-UMBCEEA) was proposed. Firstly, equivalent noise and Coordinated Multi-Point (CoMP) estimated channel were gotten by DeModulation Reference Signal (DMRS) sequence, and the Interference Rejecting Combining (IRC) filtering matrix of CoMP channel was deduced; Secondly, an equivalent interference model was established and the average inter-cell interference was obtained by using IRC filtering matrix; Finally, interference level of user in each cell to non-CoMP set was calculated, and a joint processing against strong interference users was made. In the comparison experiments with Uplink Multi-Base Cooperative Algorithm of Optimal Water Filling Control (UMBCA-OWFC), the normalized average interference of ICIR-UMBCEEA decreased by 19.2% in center users and 24.5% in edge users, and the energy efficiency of it increased by 25.48% in center users and 18.03% in edge users; ICIR-UMBCEEA had less energy consumption, and had higher throughput in center users and not much difference in edge users. The theoretical analysis and simulation results show that ICIR-UMBCEEA can effectively improve the energy efficiency of communication system in engineering.