A method for merging surface skin three-dimensional (3D) data includes the following steps: 1. constructing actually-measured 3D data of a workpiece and 3D data of a design model of the workpiece; 2. calculating a normal vector, a neighborhood radius, and a position of a sphere center of each point in the design model 3D data; 3. finding closest points to the design model 3D data for all points in the actually-measured 3D data; 4. calculating a static closest distance and a dynamic closest distance from each point in the actually-measured 3D data to the closest point in the design model 3D data; 5. constructing an objective function of a surface adaptive distance; 6. minimizing the objective function and calculating a differential motion screw; and 7. updating the actually-measured 3D data and achieving data merging.