We propose a method of measuring the three-dimensional (3D) deformation of marine propellers based on 3D digital image correlation technology. The measurement system is composed of a binocular stereo cameras, a flash, and a synchronization device, and a propeller is loaded by a cavitation tunnel. First, the self-calibration method based on epipolar constraint is used to calibrate the external parameters of the system to obtain the 3D displacement distribution of the blade surface. Then, the point cloud registration is performed on the reconstructed hub, we acquire the translation vector and rotation matrix of the point cloud at the deformed blade root to eliminate the rigid body displacement caused by different hub positions. Finally, the refracted light paths through air, glass, and water are constructed, and refraction correction is performed on the reconstructed 3D coordinates of the object point to obtain the real 3D shape of the blades in the cavitation tunnel. Measuring the propeller deformation in the cavitation tunnel with our method can get the full-field 3D displacement distribution of the propeller blades at a fixed phase, which provides a feasible non-contact full-field scheme for measuring the deformation of marine propellers.