The complexity of demand response, energy supply and load will bring uncertainty to the operation of heterogeneous energy systems. Therefore, this paper proposes an operation evaluation strategy to analyze the energy flow of heterogeneous energy systems considering the system uncertainty. Firstly, the energy flow probability model of heterogeneous energy system composed of electrical, gas and thermal energy subnets is proposed, and the coupling equipment between subnets is considered. 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 systems. The proposed method is tested in the simulation. Compared with the traditional method, the proposed method has a great improvement in solving speed and accuracy.