Emerging enterprises generally adopt a comprehensive management mode by integrating administration with safety management in operation, which in turn leads to multiple new safety problems during their production and processing of new organic materials. In order to avoid subsequent accidental risks, an emerging enterprise of Zhejiang province was taken as an example in this study, and the risk assessment on the hazard sources and harmful factors in its materials, technical process, equipment and maintenance through on-site investigation, qualitative analysis and quantitative assessment was carried out. High-risk factors of hazardous materials dispersion, fire and explosion accidents triggered in the production and processing of the enterprises were obtained based on field investigation, the result of which were quantitatively evaluated by Dow’s F&EI model. Their highest risk level of accident as “Very Risky” was determined, with an exposure to a danger zone of over 5 709.05 m2. On this basis, multi-level comprehensive risk control countermeasures were developed in this study, in aspects of safety culture development, risk prevention and control technology and accident emergency disposal. With a series of complement safety measurement, the accident risk of the enterprise production and machining was reduced below “Slight” and the exposure to hazardous area was managed within 1 315.73 m2.