The diversification of business forms leads to functional and spatial complexity in cities. The efficient determination of the complexity of an urban system is the basis for the scientific monitoring of the multi-functional aggregation within cities. Previous studies on the urban spatial structure were limited by the difficulty of collecting micro-data and the high time cost, and they focused on the macro-spatial structure, lacking fine-grained investigations of the micro-spatial structure. Additionally, high-resolution remote sensing images, which mainly rely on the textural characteristics of the spectrum of ground objects, cannot detect the social and economic functions of ground objects. Thus, it is difficult to meet the actual needs of urban planning and management. The purpose of this paper is to automatically identify the spatial heterogeneity and temporal variation of urban land use functions in the context of complex urban systems. The TF-IDF (term frequency–inverse document frequency) algorithm, a machine learning classification algorithm, and other methods are applied to identify the urban functions and distribution characteristics of the main urban area based on the POI (point of interest) data and urban form data. The results show the following: (1) From 2012 to 2022, all types of land use in Yiwu city grew at different rates, with logistics and warehousing space growing the fastest, which is in line with Yiwu’s goal of building a national logistics center for trade and services. (2) The residential area has a spatial structure with a dense central circle and a scattered periphery extending from northeast to southwest and from east to west. (3) The commercial service sector shows clear spatial differentiation between the core and the periphery. The commercial functional areas of Niansanli, Houzhai, and Chengxi, where the number of commercial POIs is relatively small, are located at the intersection of the administrative subdistricts near the city center, indicating that the commercial economic activities of the downtown subdistrict have a certain spillover effect on adjacent subdistricts. (4) The public facilities of each subdistrict are generally located in the core of each subdistrict, which ensures better convenience and accessibility. (5) Industrial land with a large total area that is scattered and mixed with urban residential land gradually tends to be centralized, forming an industrial belt around the city. This study comprehensively considers the aggregation relationship between urban buildings and land use and improves the accuracy of land identification and functional zoning.