The transmission lines are exposed to the atmosphere nature and will be affected by adverse weather such as lightning storm, so that it will affect the reliability of transmission system. This paper studies the fault probability model of transmission line during the lightning storm, and evaluates the short-term reliability of transmission system in the forecasting weather condition. Firstly, build the lightning strike fault probability model of the transmission line based on historical lightning record information, then calculate the lightning strike probability under the forecasting weather conditions, furthermore evaluate the reliability index of transmission system. Utilizing IEEE RTS-79 system to verify the validity of the proposed model and the results show that lightning has great negative influence on the transmission lines and the reliability of transmission system. The reliability evaluation model proposed in this paper can guide the short-term operation and online scheduling for transmission system operators.