Laser scanning differential confocal microscopy measurement method is characterized with its nanoscale axial measurement precision. However, the method suffers potential low lateral resolution because its signal is acquired at defocusing positions. Furthermore, its measurement speed is limited by the sequential scanning of a laser beam. The structured light illumination microscopy imaging method based on spatial light phase modulator can achieve superhigh lateral resolution imaging, but does not have a matching high axial measurement precision. Therefore, neither of these two methods meet the requirement of online, onsite measurement of the microscopy surface topography of complex object in micronano machining manufacturing process. In this paper, combining the spatial light phase modulated structured light illumination microscopy imaging technique with differential axial measurement method, a parallel objectside differential rapid measurement method based on structured light illumination is proposed. The method uses only an area array camera as the detector to acquire multiple phase images of a sample at opposite but equal distance away from the focal plane under the structured light illumination phase modulated mode. The acquired images are then synthesized to obtain corresponding high resolution images, IA and IB at opposite defocused positions respectively. The differential signal ID is calculated as the difference between the two images. The surface heights of the sample at different positions can be obtained according to the precalibrated differential curve. The proposed method was applied to measure a standard block with the step height of 500 nm at the pitch of 10 μm. The experiment results show that the proposed method achieves the standard deviation of 2.8 nm and the relative error of about 0.6%; it takes only 65 ms to complete the surface topographical measurement with the image resolution of 2 048×2 048. The measurement results show that the method is suitable for fast online nanoscale high precision axial measurement, and can achieve fast 3D topographical nanoscale precision measurement with a speed of 15/s.