Abstract The slat gear rotary actuator of civil aircraft needs to meet the requirements of small space and large transmission ratio. The planetary gear system based on triple teeth is a common actuator design, and the design structure is complex, so its tolerance control is also strict. In order to meet the design requirements of its internal structure, this paper presents a deviation analysis method for the internal structure design of a typical civil aircraft slat gear rotary actuator. The results of preliminary tolerance distribution and improved tolerance distribution are analyzed using the Jacobi-based assembly deviation model. By comparing the standard deviation of the analysis results, the validity of this deviation analysis method is verified, which proves that this method can be used to analyze the internal structure deviation of the rotary actuator of slat gear in civil aircraft.