In order to evaluate the energy efficiency of boiler systems scientifically and comprehensively, a fuzzy comprehensive evaluation method was proposed. From the angle of technical economy in engineering practice, the energy efficiency of boiler systems was defined as the primary target layer. The fuel level, equipment level and operation condition were selected and adopted as the secondary criterion layer. The specific factors were classified and applied as the tertiary index layer. By analyzing the factors' directivity effect on system energy efficiency, membership functions were determined. And the weight vector was obtained by the expert group review. So, a complete fuzzy comprehensive evaluation system was established. It can be used to quantitatively analyze the efficiency of boiler systems, as well as to evaluate the current utilization situation of energy efficiency in certain layer. It can provide advices for the subsequent optimization and the working condition comparison among units.