Laser Scanning Confocal Microscope(LSCM)，which is also called ‘Cell CT’, can be used to acquire image stacks of live cancer cells. These images are of great significance to fulfill the 3D-visualization on cell level. In this study, we proposed a 3D interpolation method based on contour points in polar coordinate system. In the new method, the origin of coordinate system is chosen to be the morphological center instead of the traditional geometric center. Resample the contour points by polar angle first, then fit the discrete points with uniform cubic B-spline to perform the interpolation, which will integrate multi-slice counter shape information. For a common nucleus structure, branched nucleus, a special method combining image morphological methods and corner detection methods based on curvature scale space is considered to solve contour division issue, and their correspondence problem was solved through a threshold radius method. The 3D reconstruction result shows much smoother and natural surface of cells and nucleus. This interpolation method is good for precise measurement of cell morphology and clinic study as well.