The fiber-optical confocal scanning interference microscope with a simple configuration was constructed with a 4-port fiber-optic coupler, and the new method based on the phase shifting method was proposed for surface profiling by the system. In the method, the height of a specimen was determined from the phase of confocal beam. It was verified experimentally that the method was applicable to even the confocal interference microscope with a long-wavelength source and a low NA objective, and that the scanning time could be drastically reduced compared with the conventional method. Finally, it was found that our method is less sensitive to the variation of surface reflectivity than the conventional method.