This study investigated the perception of numbers in humans in 3D stimuli. Recent research has shown that number processing relies on “number sense” for small values, in line with Weber’s law. While previous studies have reported 3D numerosity overestimation mainly in higher numerical values, our experiment examined whether this phenomenon occurs at lower numerical values. We also explored whether the Weber ratio follows Weber’s law when comparing 2D and 3D stimuli in terms of the number of elements. Observers were presented with pairs of stimuli on a monitor and were asked to identify the stimulus with a larger number of elements. Using the constant method, we calculated the point of subjective equality (PSE), just noticeable difference (JND), and Weber ratios from the collected data. As a result, it was confirmed that the phenomenon of over-estimation of 3D numerical values occurs even when the numerical values are small. Additionally, we observed that the Weber fraction adhered to Weber’s law within the measured range. These findings contribute to the existing body of research, supporting the existence of distinct mechanisms for perceiving numerosity and density.