As two of the most complete existing examples of royal architecture and cultural World Heritage Sites in China, the Beijing Forbidden City and the Shenyang Imperial Palace are distinctive in terms of their spatial organization. This study used the relational diagram method of space syntax theory to quantitatively analyze the spaces of these two palaces. Furthermore, the characteristics of these spaces were explored by comparing the integration and depth value of each palace space, as well as the differences in architectural culture between the different times and nationalities that they reflect. The results show that in the Forbidden City, office space had the lowest degree of spatial enclosure (depth value), while living space had the highest spatial enclosure. Moreover, there was little difference in accessibility (integration value) among office space, living space, and recreation space. In the Shenyang Imperial Palace, the accessibility of office space, living space, and recreation space showed a decreasing trend, while their spatial enclosure showed an increasing trend. The depth values of office space, living space, and recreation space were higher in the Beijing Forbidden City than in the Shenyang Imperial Palace by 245%, 109%, and 35%, respectively. The integration value of office space was 22.2% higher in the Shenyang Imperial Palace than in the Forbidden City, while the integration values of living space and recreation space were higher in the Forbidden City than in the Shenyang Imperial Palace by 13.9% and 49.2%, respectively. The degree of enclosure of the recreation spaces in both palaces was very strong, indicating that the royal family paid attention to privacy during their leisure activities. In the process of use, the functional conversion of different palaces in the Forbidden City significantly improved the accessibility of both the emperor’s living space and the minister’s office space and simultaneously strengthened the connection between these two spaces. Factors in the construction sequence led to the unreasonable accessibility of recreation space in the Shenyang Imperial Palace.