The size of a city is not only essential for depicting the scale of the urban system, but also crucial to support the prosperity, order, and high-speed developments. However, its relation to the underlying urban structure has not been empirically investigated in detail. To examine the impact of city size on the city structure and quantify structural features, in this study, a statistical analysis was performed based on network science and an interdisciplinary theoretical system. To obtain the statistical law of internal node layout, the urban system was regarded as a complete graph weighted by the Euclidean distance. The relationship between the urban internal nodes layout (points of interest data, Weibo check-in data, and central point of road intersection data) and the city size was established. The results confirmed the existence of statistical laws in the layout of urban spatial elements, and explored the relationship between the changes in urban node network structure and inequality. This study provided a new perspective of urban structure to understand the complexity of the city, and suggested an approach to adjust this structure to narrow down the gap between the urban and rural areas.