The work aims to study the influence rule of the changed section structure on the compressive strength of polygonal corrugated box. The compression test was done by changing the number of vertical side plates, side length, and enclosed angle of adjacent side plates. The deformation failure process and the change law of compressive strength of the polygonal box were analyzed. The calculation model with its side length of independent vertical side plate replacing the perimeter was established. When other conditions that affected the compressive strength of the box remained constant, the compressive strength was increased with the increase of the number of side plates. When the number of side plates was equal to that of the corrugated box, the side length of side plate was closer to the regular polygon, the enclosed angle was closer to 135°, and the compressive strength was greater. The deformation failure of the corrugated box is essentially caused by the overall unstability of the side plate structure under stress. The proposed calculation model can more accurately reflect the mechanical property of the box under stress and effectively characterize the compressive strength of the polygonal corrugated box.