The large-area and long-distance precision measurement and data processing become the developing direction of ship construction precision control technology. Based on the point cloud data obtained by measuring the deck planeness with the total station scanner at multiple stations, an efficient planeness calculation method is proposed. The point cloud data and common point coordinates (targets) obtained from the total station scanner at multiple stations are used to solve, and the coordinate system transformation parameters are calculated to complete the coordinate system unification; the least square method is used to complete the plane fitting, and the planeness result is obtained by rotating the fitting surface. The MATLAB simulation is used to verify the accuracy and effectiveness of the calculation method, which shows that it is suitable for the planeness measurement of large-area deck.