A miniaturized non-destructive optical system for measuring the 3D flaws of inner surface of a pipe is proposed,which is based on Fourier transform profilometry (FTP) using two microscopes and an amplitude grating. It is possible to get a magnified and clear image of a small object by using a microscope. The images of the inner surface of pipe can be non-contact captured in real time when the sensor is moving along the pipe driven by a micro-robot. Experimental results show that the reconstruction of 3D surface of the inner surface is obtained with high precision. This method can be used to measure the 3D shape of pipe inner surface,so it should be interesting for practical applications.