Skin waviness near the static pressure source affect the accuracy of altitude measurement and the airworthiness of the aircraft's RVSM operational capability. Therefore, it is necessary to evaluate the effect of small-scale skin waviness. A fast analysis method based on the small disturbance hypothesis and a numerical calculation method based on CFD were established to study the pressure effect of the waviness, and the methods were verified by the wind tunnel test data. The results show that the numerical calculation method can be used to evaluate and analyze the effects of skin waviness with high accuracy. According to the statistical analysis, the pressure deviation between the calculated value and the test value of 97.8% of the 900 pressure-measuring holes is within ± 0.002. The influence of pressure on skin waviness can be obtained accurately and quickly by the modified fast analysis method, which can be used as a rapid evaluation method for related engineering problems.