The accurate identification of pills is essential for their safe administration in the medical field. Despite technological advancements, pill classification encounters hurdles such as ambiguous images, pattern similarities, mixed pills, and variations in pill shapes. A significant factor is the inability of 2D imaging to capture a pill’s 3D structure efficiently. Additionally, the scarcity of diverse datasets reflecting various pill shapes and colors hampers accurate prediction. Our experimental investigation shows that while color-based classification obtains a 95% accuracy rate, shape-based classification only reaches 66%, underscoring the inherent difficulty distinguishing between pills with similar patterns. In response to these challenges, we propose a novel system integrating Multi Combination Pattern Labeling (MCPL), a new method designed to accurately extract feature points and pill patterns. MCPL extracts feature points invariant to rotation and scale and effectively identifies unique edges, thereby emphasizing pills’ contour and structural features. This innovative approach enables the robust extraction of information regarding various shapes, sizes, and complex pill patterns, considering even the 3D structure of the pills. Experimental results show that the proposed method improves the existing recognition performance by about 1.2 times. By improving the accuracy and reliability of pill classification and recognition, MCPL can significantly enhance patient safety and medical efficiency. By overcoming the limitations inherent in existing classification methods, MCPL provides high-accuracy pill classification, even with constrained datasets. It substantially enhances the reliability of pill classification and recognition, contributing to improved patient safety and medical efficiency.