Scanning electron microscopy (SEM) has an important application in the petroleum field, which is often used to analyze the microstructure of reservoir rocks, etc. Most of these analyses are based on two-dimensional images. In fact, SEM can carry out micro-nano scale three-dimensional measurement, and three-dimensional models can provide more accurate information than two-dimensional images. Among the commonly used SEM 3D reconstruction methods, parallax depth mapping is the most commonly used method. Multiple SEM images can be obtained by continuously tilting the sample table at a certain Angle, and multiple point clouds can be generated according to the parallax depth mapping method, and a more complete point clouds recovery can be achieved by combining the point clouds registration. However, the root mean square error of the point clouds generated by this method is relatively large and unstable after participating in point clouds registration. Therefore, this paper proposes a new method for generating point clouds. Firstly, the sample stage is rotated by a certain angle to obtain two SEM images. This operation makes the rotation matrix a known quantity. Then, based on the imaging model, an equation system is constructed to estimate the unknown translation parameters, and finally, triangulation is used to obtain the point clouds. The method proposed in this paper was tested on a publicly available 3D SEM image set, and the results showed that compared to the disparity depth mapping method, the point clouds generated by our method showed a significant reduction in root mean square error and relative rotation error in point clouds registration.