Large-scale grid connection of new energy power generation makes cogeneration units need flexible operation to smooth out the fluctuation brought by new energy access. In order to meet the control requirements of flexible operation of the unit and the safety of the unit operation, a flexible control strategy for cogeneration units based on flexibility evaluation is designed. Firstly, according to the response characteristics of electrical load, thermal load and throttle pressure of the unit, a calculation method of flexibility evaluation indexes which can represent the load adaptability and operation safety of the unit are proposed, and these indexes are used as the basis for selecting the optimal flexibility factors. Then, the influence of flexibility factor on the system performance under a single working condition is simulated. Finally, on the basis of determining the optimal flexibility factors under different working conditions, the adaptive flexibility factors that changing with working conditions are designed and applied to the flexible control. The simulation results show that, the control strategy can not only achieve a better control effect when the unit runs under large-scale conditions change, but also achieve a better control for the unit after the low-pressure cylinder is cut off, which can meet the control requirements of flexible operation of the unit and ensure the safety of the unit operation..