The invention discloses a construction method of a large-span variable cross section tunnel intersection, and presents a set of construction techniques, such as the 'gradual change of arch elevation',the 'side wall widened section', the 'reduced excavation section', the 'arc guide hole combined portal arch' and the like, and forms a complete set of large-span variable cross section tunnel intersection construction technology. The construction method solves the construction problems of the vault elevation difference of two cross tunnels and the mutual influence of steel arch frame erection ofthe intersection. The construction risk of large-span excavation is reduced, and the construction transformation and smooth transition from a small cross section tunnel to a large section tunnel are realized. The construction method is widely used in cross-tunnel with large span, change of cross-section, development of joint fissure, low strength of surrounding rock and low self-stability. According to the construction method, the construction period can be effectively guaranteed and the safety and overall stability of the large-span variable cross section tunnel construction can be ensured.