With the development of civil aviation, composite materials are widely used in civil aircraft nacelle design. Due to the electrical conductivity and lightning damage resistance of carbon fiber composites are not as good as aluminium structure, the lightning protection capability of the nacelle composite structure has become a key problem affecting the flight safety of aircraft. In this paper, according to the airworthiness regulations and the corresponding international standards, the testing verification method of composite material lightning protection for civil aircraft nacelle was described, and the damage effect of paint thickness was studied. The lightning test results of composite test specimens which represent the conventional configuration of the nacelle skin with different paint thickness show that when the paint thickness is relative thin, the paint layer has no obvious effect on the lightning protection ability; when the paint reaches a certain thickness, the thicker paint layer will significantly reduce the lightning protection ability, and in the most serious condition, it will cause the penetration of the composite skin and damage the inner system, which will cause flight safety hazard. The experimental results are well consistent with the theoretical analysis, which provides guidance and reference for the lightning protection design of composite structure of civil aircraft nacelle.