The distributed renewable energy system, integrating various renewable energy resources, is a significant energy supply technology within energy internet. It is an effective way to meet increasingly growing demand for energy conservation and environmental damage reduction in energy generation and energy utilization. In this paper, the life cycle assessment (LCA) method and fuzzy rough sets (FRS) theory are combined to build an environmental evaluation model for a distributed renewable energy system. The ReCiPe2016 method is selected to calculate the environmental effect scores of the distributed energy system, and the FRS is utilized to identify the crucial activities and exchanges during its life cycle from cradle to grave. The generalized evaluation method is applied to a real-world case study, a typical distributed energy system located in Yanqing District, Beijing, China, which is composed of wind power, small-scale hydropower, photovoltaic, centralized solar thermal power plant and a biogas power plant. The results show that the environmental effect of per kWh power derived from the distributed renewable energy system is 2.06 × 10−3 species disappeared per year, 9.88 × 10−3 disability-adjusted life years, and 1.75 × 10−3 USD loss on fossil resources extraction, and further in the uncertainty analysis, it is found that the environmental load can be reduced effectively and efficiently by improving life span and annual utilization hour of power generation technologies and technology upgrade for wind turbine and photovoltaic plants. The results show that the proposed evaluation method could fast evaluate the environmental effects of a distributed energy system while the uncertainty analysis with FRS successfully and effectively identifies the key element and link among its life span.