The high-quality development of new agricultural business entities (NABEs) is an important driving force for realizing rural revitalization and accelerating the modernization of agriculture and rural areas. The main purpose of the study is to investigate the spatial distribution pattern, aggregation scales, development mechanism, and internal differences of various types of NABEs in different regions. It provides targeted ideas for alleviating regional differences in the development of NABEs in different agricultural regions. Kernel density estimation, nearest neighbor distance analysis, Tyson’s polygon coefficient of variation, and Ripley’s K function are used to study the spatial and temporal evolution, spatial aggregation, and scale divergence of various types of NABEs, and Pearson correlation analysis is incorporated to explore the specific factors affecting the development of various types of NABEs. The study results: First, family farms are the most widely distributed, and agricultural enterprises are the most sparsely distributed, being distributed “more in the southeast and less in the northwest” in all three categories. Second, the strongest aggregation scales of different NABEs are increasing, and the strongest aggregation scales of agricultural enterprises are larger than those of family farms and cooperatives in all agricultural areas. Third, the development of specialized farmers’ cooperatives (abbreviated as ‘cooperatives’) is more constrained by traditional agricultural inputs and is a kind of agricultural input-oriented development. Family farms are more constrained by the living standards of rural residents in the region and are a kind of rural economy-oriented development. Agricultural enterprises are more subject to the economic level of the region, which is a kind of market economy-oriented development. Finally, in the process of developing NABEs, regional differences should be emphasized, and a small number of agriculturally leading enterprises and model cooperatives should drive a large number of small-scale family farms and smallholder farmers in order to become a characteristic path for China’s agricultural development.