Along with the rapid increase in the number of electric vehicles, more and more EV charging stations tend to have charging infrastructure, rooftop photovoltaic and energy storage all together for energy saving and emission reduction. Compared with individual design for each of the components in such kind of systems, an integrated design can result in higher efficiency, increased reliability, and lower total capital cost. This paper mainly focuses on the tertiary control strategy for dynamic state operation, such as PV generation fluctuation and random arrival/leave of EVs. The tertiary control aims to achieve stable operation under dynamic states, as well as to optimize the energy flow in the station to realize maximal operational benefits with constraints such as peak/valley price of electricity, state of discharge limitation of battery, etc. In this paper, four energy management functions in tertiary control level are proposed, and their performance is verified by simulations. By using prediction of PV power and EV load in the following 72 h, a novel tertiary control logic is proposed to optimize PVC and ESC power flow by changing their droop characteristics, so that minimum operational cost for the station can be achieved. Furthermore, a sensitivity analysis is conducted for three parameters, including ES battery capacity, weather influence, and PV and EV load prediction error. The results from sensitivity analysis indicate that ES battery capacity and weather condition lead to a great impact on the operational cost of the integrated charging station, while a typical prediction error of PV power and EV load will not influence the optimization result significantly.