Traditional building energy evaluation methods usually adopt a single energy use indicator as the benchmark. However, such single-indicator based methods often lead to a paradox that switching off building service equipment or systems is equivalent to energy saving. To avoid such paradox for a more pragmatic and comprehensive evaluation of building energy use, this paper aims to establish a robust evaluation model of the operational energy efficiency for public buildings by coupling the analytic hierarchy process (AHP) and fuzzy comprehensive evaluation (FCE). Firstly, 23 quantitative indexes and 7 qualitative indexes are extracted from existing building energy codes/standards in the input-output perspective of energy performance evaluations for public buildings. The AHP is then used to determine the weight of each index based on a proposed index correction method, which extends the range of applicability of the index system. Finally, a three-level comprehensive evaluation model is established for the operational energy efficiency of public buildings. Furthermore, a case study is conducted on a typical office building to validate the evaluation results with the proposed model. The case building achieves an overall score of 84.9 at a “Good” level, and corresponding recommendations are made for further improving building performance indexes. The proposed method is of great significance to developing building energy efficiency assessment systems and guidelines in China and over the world. •A comprehensive evaluation system of building energy efficiency is established.•The evaluation method of building energy efficiency is based on energy input-output.•Analytic hierarchy process combined with fuzzy comprehensive evaluation method is adopted.