In cone-beam computed tomography (CT) systems, due to the difficult placing of the rear collimator, uncorrected scatter signals can cause a deviation of the measured values from the true ones, reducing the image contrast and signal-to-noise ratio and even producing artifacts. However, a beam stop array (BSA) can be used to effectively estimate the scatter signal distribution after the beam passing through the sample. In this study, the BSA correction method is applied for a cone-beam micro-CT system; the scatter distribution is obtained by placing a correction plate between the X-ray source and the sample. First, the basic principle of BSA-based scatter correction is introduced and the specific experimental devices and steps are given. Then, several samples are analyzed with an independently developed cone-beam micro-CT system. Finally, the quality of the obtained images is evaluated based on digital radiography projections, reconstruction slices, three-dimensional reconstruction images, and so on. Results show that the BSA correction method can effectively reduce the scatter artifacts in cone-beam micro-CT systems and improve the image quality, which verifies the feasibility of applying BSA correction method to cone-beam micro-CT systems. Given the low energy of the X-ray source and the large influence of the focus drift, beam-hardening correction and focus-drift correction are also included, further improving the image quality.