The relative dynamical equations of the missile and target on an attack plane of the parallel approaching method are extended to the three-dimensional space in this paper. The calculation formulas of the trajectory obliquity and drift angle are deduced through the relative dynamical equations of the missile and target, and multi-section trajectory generation method is presented. Then, by integrating with the equations of atmospheric motion (MM5 equations), the guidance trajectory model of the parallel approaching method is established under the non-standard weather conditions. Through comparison the guidance trajectory of parallel approaching method under the standard and non-standard weather conditions is analyzed, the result shows that the headwind mainly influences the missile's range and the crosswind influences the missile's direction mainly. Finally, the visual simulation of an air-to-air missile's guidance trajectory under two different weather conditions by the STK (Satellite Tool Kit) is realized, which exhibits the motion trajectory of the missile approaching and hitting the target vividly.