The airworthiness clause about the drainage of APU compartment requires more than 90% of the liquid to be discharged through the structure within 10 min without additional fire risk. Because the door is the main drainage structure of APU compartment, in order to meet the airworthiness requirements, there has been research work on the drainage analysis method of civil aircraft APU door. From the perspective of the overall structure layout, assuming that there is a known and unique discharge port in the wholeAPU compartment, the relationship between the discharge port size and the discharge rate was discussed and analyzed. However, there is little discussion on the discharge capacity of the local structure. When the APU door adopts the sectional seal layout, the inappropriate structure shape and unsuitable size design may lead to the leakage of combustible liquid from the seal gap which will increase the risk of accidental fire. Therefore, the drainage design of the local structure is also very important for the safe and effective discharge of liquid in the compartment. Based on the liquid discharge requirement of APU door of civil aircraft, this paper analyzes the liquid discharge capacity of local hydrops structure of the door as well as the related influencing factors, determines the design points for such factors and gives the corresponding structural optimization measures.