The invention relates to the technical field of photovoltaic micro-grid control, and particularly discloses a real-time coordination and control method of a photovoltaic micro-grid system. A central real-time optimal control layer and a local control layer are involved in the real-time coordination and control method. The central real-time optimal control layer collects the voltage and frequency of an AC bus of the photovoltaic micro-grid system, the charge state of a storage battery pack, the output power of photovoltaic power generation micro-sources, the output power of the storage battery pack, the output power of a super capacitor and the real-time power of a load in real time, generates a real-time coordination and control strategy and a secondary frequency modulation and scheduling plan, and issues the strategy and the plan to all local controllers. The local control layer coordinates and controls all the micro-sources in real time, and particularly achieves the scheduling plan issued by the central real-time optimal control layer. According to the real-time coordination and control method, a micro-grid central optimizing controller can manage, coordinate and control all the local controllers in a unified mode, the micro-grid can efficiently and economically run, the output power of the photovoltaic power generation unit is utilized to the maximum extent, the output power fluctuation and the tracking load change of the photovoltaic power generation unit are restrained, the running method of the micro-grid is reasonably adjusted, and energy balance is achieved.