3D imaging and metrology of complex micro-structures is a critical task for precision manufacturing and inspection. In this paper, an accurate and flexible calibration method for 3D microscopic structured light system with telecentric imaging and Scheimpflug projector is proposed. Firstly, a fringe projection 3D microscopy (FP-3DM) system consisting of a telecentric camera and a Scheimpflug projector is developed, which can take full advantage of the depth of field (DOF) and increase the measurement depth range. Secondly, an accurate and flexible joint calibration method is proposed to calibrate the developed system, which utilizes the established pinhole imaging model and Scheimpflug distortion model to calibrate telecentric imaging, and fully considers the correction and error optimization of the Scheimpflug projection model. Meanwhile, the optimized local homography is calculated to obtain more accurate sub-pixel correspondence between the camera and the projector, and the perspective-n-point (PnP) method make the 3D coordinate estimation of the feature point more accurate. Finally, a prototype and a dedicated calibration program are developed to realize high-resolution and high-precision 3D imaging. The experimental results demonstrate that the re-projection error is less than 1µm, and the 3D repeated measurement error based on feature fitting is less than 4µm, within the calibrated volume of 10(H)mm × 50(W)mm × 40(D)mm.