This paper chooses the Changjiang Middle Reaches Megalopolis as the research object，takes the city cluster logistics system as a symbiotic system，evaluates its symbiotic energy generation level. Firstly，the paper has defined the scope of the Yangtze River middle reaches city cluster. Secondly，this paper has evaluated the system’s symbiotic energy generation level using the Malmquist total factor productivity index model，and constructed the influencing factors Tobit regression analysis model，in order to clear the key factors which influence the system’s symbiotic energy generation level. Finally，according to the evaluation results，the corresponding countermeasures and suggestions have been put forward，which includes the enhancement of city cluster logistics symbiotic system’s symbiotic units subject abilities，the ascending of city cluster logistics symbiotic system’s symbiotic interface，the optimization of city cluster logistics symbiotic system’s symbiotic environment and the specific measures.