Operation modes of combined heat and power (CHP) units are closely related to the economic benefits of energy application in integrated energy station. In this paper, a novel bi-level optimal configuration method is proposed considering different operation modes of CHP, and a life-cycle assessment system on economic and environmental benefits is constructed using system dynamics (SD) method. Firstly, the basic structure and operation issues of a typical integrated energy station employing CHP are addressed. Secondly, the bi-level collaborative optimization model of the integrated energy station is constructed to minimize the annualized cost considering three operating modes, namely following the thermal load (FEL), following the electric load (FTL) and switching adaptively between FEL and FTL. Then, the model is solved by the column-and-constraint generation and particle swarm optimization coordination with mixed-linear integer programming respectively. Subsequently, the sensitivity of CHP units heat-to-electric ratio and electric storage to the planning results are analyzed in detail. Finally, case studies are carried out based on an actual integrated energy station. The optimization results show that, compared with FEL and FTL operating modes of the CHP units, the annualized cost of the system under adaptive operation mode is reduced by 26.5% and 42.8%, respectively. Besides, the assessment of the optimized system indicates that the total profit and carbon dioxide emission reduction of the station during its life-cycle are expected to reach 28.53 million CNY and 25.33 ten thousand tons respectively, which provides a reference for decision-making and a basis for flexible operation.