The invention discloses a method and device for marking the center of rotation based on an optical projection tomography sinogram. The method includes: the projection rotation center of the marker and the sample is the same, the first section sinogram and the second section sinogram are obtained, and the calculation The balance position of the first section sinogram is calculated by calculating the distance from the balance position to the upper edge and the lower edge of the first section sinogram to obtain the target height value, and the second section sinogram is longitudinally cut or longitudinally repaired, so The height values of the longitudinal cropping and the longitudinal repairing are the target height values, and the back projection reconstruction is performed on the sinogram of the second section after the longitudinal cutting or longitudinal repairing to obtain the target reconstructed cross-sectional view of the sample. The invention quickly calculates the projection rotation center of the sample by introducing markers as reference objects without being affected by the complexity of the sample structure, realizes the correction of the projection rotation center, reduces the artifacts of the reconstruction section, and improves the imaging quality.