The invention discloses a long-span variable section tunnel secondary lining trolley and a construction method thereof. The trolley comprises a main portal frame and a secondary portal frame, and the secondary portal frame and the main portal frame form a horizontal type E-shaped structure. The top of the secondary portal frame is connected to a formwork beam through upper longitudinal girders, formwork columns are arranged on the formwork beam, and the upper ends of the formwork columns abut against a formwork at the top of a lining section. The main portal frame and the secondary portal frame are placed on three steel rails, beams of the secondary portal frame, the formwork columns and the formwork beam are each provided with a disjunction joint, a connecting plate is arranged detachably at each disjunction joint, and traction driving wheels are arranged on the two outer steel rails. When the lining section changes, the transformation of the section of the trolley can be completed only through a small amount of disassembly of the formwork, the formwork columns and the secondary portal frame, the time for putting the trolley in place is greatly reduced, the construction safety risk is lowered and a lot of manpower is saved; by arranging the disjunction joints, the time for field remanufacturing is reduced, the transformation of the trolley is accelerated, and the construction safety risk is lowered.