The invention discloses a molding method of a double-curvature variable-section variable-thickness through beam. The molding method comprises the steps that a molding die is manufactured according to the structural form of the double-curvature variable-section variable-thickness through beam; the molding die comprises a combined female die body and a limiting strip, and the combined female die body comprises a detachable side check block and a fixed block; prepared hot-melting prepreg and hot-melting prepreg cloth are shorn to the size of an unfolded section laying layer of the through beam, a hot-melting prepreg cloth laying layer is firstly laid on the surface of the female die body, and then vacuumizing compaction is carried out; laying layers are stacked according to the thickness of the through beam and the designed laying layer sequence, hot-pressing shaping is carried out in the laying layering stacking process according to the thickness of the laying layers, and finally a composite material prepreg lamination is manufactured; then coating, curing and combined female die body removal are carried out to obtain a product. The aerodynamic configuration requirement can be effectively guaranteed, the problems that the laying layers and size precision of a large-size double-curvature variable-section variable-thickness through beam are hard to control are solved, and finally the overall quality and size precision requirements of the through beam are guaranteed.