The invention discloses a comprehensive energy system energy efficiency analysis method and system considering energy flow links, and the method comprises the steps: S1, analyzing the electric, hot and cold energy flow paths of a comprehensive energy system, dividing the energy flow links of the comprehensive energy system, and obtaining an energy flow model of the comprehensive energy system; S2, based on the energy flow model, analyzing the energy utilization efficiency of the integrated energy system from each energy flow link of the integrated energy system; S3, based on an analysis result, obtaining an energy utilization efficiency analysis calculation expression of the integrated energy system; and S4, analyzing the energy efficiency of the integrated energy system by adopting the calculation expression. Energy supply, conversion, transmission, storage and demand links of the comprehensive energy system are considered, flow of electric / hot / cold energy in the comprehensive energy system is analyzed, then the energy utilization efficiency of the comprehensive energy system is obtained, and the energy efficiency of the comprehensive energy system can be completely analyzed.