Three-dimensional simulation of tolerance for structural assembly can be used to simulate tolerance accumulation during the assembly process before components are manufactured. This helps in guiding tolerance design of aircraft via iteratively optimizing the model, thus avoiding significant deviations in aircraft assembly, and extra time and material costs can be saved. Three-dimensional tolerance simulation analysis helps in predicting whether the controlling objectives can meet engineering requirements during the radome nose assembly process, which can be challenging using traditional one-dimensional size chain methods. The probability of deviation happens in the gap between the nose and radome was reduced from 3.19%~6.31% to 0.10%~0.75% via optimization based on simulation result, and the probability of deviation happens in the step difference between the radome and nose was reduced from of 0.31%~1.81% to 0~0.11%. The results of three-dimensional simulation research of tolerance provides guidance for designer and technician in radome and nose development and production.