The hybrid energy system (HES) has attracted more and more attention since it can not only achieve multi-energy supply but realize cascade utilization of energy resources. However, the performances of the HES in relation to economic, environmental, social, and technological aspects are rarely studied. Therefore, this paper tries to fill this research gap to evaluate the sustainability performance of an HES. First, an evaluation criteria system is established based on a literature review. After that, the group analytic hierarchy process (GAHP) technique is used to obtain the importance weights of these criteria. Later, the sustainability performance of the HES is calculated through an improved fuzzy synthetic evaluation (FSE) approach based on a cloud model. The applicability of this approach is demonstrated by a real case study in Zhejiang province, China. Finally, the sensitivity analysis results reveal that the overall consequence is that the performance of an HES is robust when the criteria weight is floating within a certain range (−30–30%), and the comparative analysis with the traditional FSE also reveals that the proposed approach is superior.