A focus detection apparatus and a method thereof are provided. In the method, a medical image is obtained. Size of a target focus and a sliding window are determined, and side length of the sliding windows is at least twice the side length of the target focus. The medical image is scanned through the sliding window, and a stride which the sliding windows moves each time is not greater than the side length of the target focus. At least one area of interest is obtained based on the scan result. Then, the area of interest is identified based on machine learning techniques, and perform candidate aggregation and multiple size aggregation to determine at least one focus position. Accordingly, the computational time and the detection accuracy can be improved.