A variety of uncertainties in heterogeneous energy system pose challenges to system operation evaluation. In this paper, an operation evaluation strategy of heterogeneous energy system is proposed, which considers the uncertainty of load, demand response and energy supply. Firstly, based on the analysis of the coupling equipment between subnets, the energy flow probability model of heterogeneous energy system composed of electrical, gas and thermal subnets is proposed. Secondly, the point estimation algorithm is used to analyze the system uncertainty. In addition, a new analysis method is proposed to accelerate the energy flow decomposition of heterogeneous energy system. The proposed method is tested in the simulation. Compared with the traditional method, the proposed method has a great improvement in solution speed and accuracy.