As an important part of aircraft manufacturing, final assembly line, how to improve and stabilize production capacity has always been a research hotspot. Based on the production capacity analysis of a transport airplane, the alarm problems in the final assembly have been normalized, and a pulsation closed-loop control model of the aircraft final assembly line has been proposed. The alarm type ratios have been used as the input variables of the control model, and the load rate and production capacity have been taken as the output parameters. The neural method has been used to construct the health status evaluation by analyzing the relationship between input variables and output parameters. According to the production capacity output of the above state evaluation model, the production capacity prediction model has been constructed using the Markov chain, which successfully evaluates the implementation of the production plan of the pulsation final assembly line and gives feedback to the pulsation controller to achieve production pulsation adjustment. Finally, the pulsation closed-loop controlling model is proved to be very effective through a practical design.