Soybean root diseases are associated with numerous fungal and oomycete pathogens; however, the community dynamics and interactions of these pathogens are largely unknown. We performed 13 loop-mediated isothermal amplification (LAMP) assays that targeted specific soybean root pathogens, and traditional isolation assays. A total of 159 samples were collected from three locations in the Huang-Huai-Hai region of China at three soybean growth stages (30, 60, and 90 days after planting) in 2016. In LAMP results, we found that pathogen communities differed slightly among locations, but changed dramatically between soybean growth stages. Phytophthora sojae, Rhizoctonia solani, and Fusarium oxysporum were most frequently detected at the early stage, whereas Phomopsis longicolla, Fusarium equiseti, and Fusarium virguliforme were most common in the later stages. Most samples (86%) contained two to six pathogen species. Interestingly, the less detectable species tended to exist in the samples containing more detected species, and some pathogens preferentially co-occurred in diseased tissue, including P. sojae–R. solani–F. oxysporum and F. virguliforme–Calonectria ilicicola, implying potential interactions during infection. The LAMP detection results were confirmed by traditional isolation methods. The isolated strains exhibited different virulence to soybean, further implying a beneficial interaction among some pathogens.