A shaft sealing system for an organic working medium turbine-gear case power generation device comprises a double-end-face contact type mechanical sealing assembly, a blocking and sealing oil station, a throttle valve, an overflow valve, a flow meter, a sealing cavity temperature sensor, a sealing cavity pressure sensor, an oil supply pressure sensor, a blocking and sealing oil supply pipeline and a blocking and sealing oil recycling pipeline. The double-end-face contact type mechanical sealing assembly is arranged on a gear case high-speed shaft and located in a turbine sealing shell. The turbine sealing shell is provided with a blocking and sealing oil supply port and a blocking and sealing oil return port. The blocking and sealing oil supply port communicates with the blocking and sealing oil station through a blocking and sealing oil supply pipeline. The blocking and sealing oil return port communicates with the blocking and sealing oil station through a blocking and sealing oil recycling pipeline, and the turbine sealing shell is provided with the sealing cavity pressure sensor and the sealing cavity temperature sensor. The blocking and sealing oil supply pipeline is provided with the overflow valve, the flow meter and the oil supply pressure sensor. The blocking and sealing oil recycling pipeline is provided with the throttle valve. According to the system, working medium leakage can be avoided, and air can be prevented from entering the power generation device.