Objective To analyze the evaluation results of health enterprises in Beijing City and their influencing factors. Methods A total of 40 enterprises that passed the health enterprise evaluation in Beijing from 2021 to 2022 were selected as the study subjects using the judgment sampling method. The total evaluation scores and influencing factors were analyzed based on the size, nature, industry classification, and establishment time of the enterprises. Results The total evaluation score of the 40 health enterprises was (553.1±18.4) points. Scores for the primary evaluation indicators, including management organization and system, occupational disease prevention measures, health environment, health promotion measures, prevention measures for occupational stress caused damage, and musculoskeletal injury prevention measures, were (94.0±4.8), (94.0±4.3), (94.5±3.8), (89.7±4.8), (89.6±4.6), and (91.4±5.9) points, respectively. The result of multiple linear regression analysis showed that, large enterprises had higher total evaluation scores than medium enterprises and micro and small enterprises after controlling for confounding factors such as industry classification and establishment time (all P<0.10). The total evaluation scores of private enterprises and foreign-funded enterprises were lower than that of state-owned or state-participated enterprises (all P<0.10). Conclusion Enterprise size and nature are influencing factors for the total evaluation score of health enterprises. It is necessary to enhance resource and policy support for medium-sized, micro and small enterprises and private enterprises to improve the development of the health enterprises.