Intensive potato continuous cropping (IPCC) results in low potato yields compared with non-intensive potato continuous cropping (PCC) and potato-maize rotation (PMRC). However, it is still unclear whether the degree of potato continuous cropping obstacle is related to the soil environment formed by the previous crop. To investigate the effect of planting potatoes and planting maize after harvesting the spring potatoes on soil chemical properties and soil microbial community structure, an experiment was carried out in the same origin soil environment over a period of seven years: (a) PCC, i.e., spring planting; (b) IPCC, i.e., autumn and spring planting (IPCC); (c) PMRC, i.e., spring potatoes and summer maize (PMRC), and (d) fallow (CK). We confirmed that the potato yield under PMRC was significantly higher than that under PCC and IPCC. Under IPCC, soil total phosphorus content was significantly higher than other treatments, whereas ammonium nitrogen content was the lowest. Compared with PCC and IPCC, PMRC had a higher ammonium nitrogen content and lower total phosphorus content. The significantly different fungal taxa in IPCC (Glomerellales, Plectosphaerella, Thelebolales) may threaten the health of the plant and positive correlated with soil total phosphorus, while other microbial taxa in PMRC (Bacillales, Polythrincium, Helotiales) can mainly promotes plant nitrogen uptake and protects plants against diseases. The PMRC-promoting taxa were positively correlated with the ammonium nitrogen content and negative correlated with soil total phosphorus content. In summary, the cropping systems might have affected potato yields by changed soil microorganism community structures – especially fungal community structures – and by the chemical properties of the soils that also depends on microbes.