Since the optimal scheduling on integrated energy systems (IES) with complex multi-energy flows can hardly balance the economy and low-carbon operation, an NSGA-Ⅱ-WPA algorithm based on non-dominant genetic algorithm (NSGA-Ⅱ) and wolf pack algorithm (WPA) is proposed. The proposed algorithm can realize the multi-objective optimization. Firstly, an IES scheduling model of strong coupling relationship is established considering the characteristics of the IES with multi-energy flows which integrates a power supply subsystem, a heat supply subsystem and a cooling supply subsystem. Secondly, the basic IES operation strategies are designed which includes the battery storage operation strategy under real-time pricing mechanism, layered energy supply strategy and carbon emission trading strategy. The strategies aim to realize the collaborative control optimization on the IES influenced by the multiple factors. Finally, the multi-objective optimization for the IES with multi-energy flows is completed based on the NNSGA-Ⅱ-WPA algorithm. The operational cost and carbon emissions of the IES are evaluated by simulation experiments, and the experimental results prove that the improvement on comprehensive energy efficiency of the IES provided by the proposed algorithm is better than that by NSGA-Ⅱ algorithm.