Taking the corn plantation area of 10 farmers in the suburbs of Beijing as the research object, soil samples from the planting period, flower spike samples from the flowering period, corn samples from the harvest period and different storage periods were taken to detect the mycoflora, microbial contamination and the mycotoxins. The results show that during the whole post-harvest natural drying period of corn, the risk of mold formation is highest in the early storage period (within one month after harvest). Among them, Fusarium has always been the dominant flora, and the toxins produced by it mainly include deoxynivalenol (DON), Zearalenone (ZEN), and fumonisin (FB1, FB2), the detection rates were 100%, 95%, and 93%, respectively, and the over-standard rates of DON and ZEN during the storage period were greater than 40%, and other toxins such as AFBs, OTA, ST, T-2, and HT-2 were not detected. In addition, the high-throughput sequencing technology was used to analyze the relationship between fungal diversity and agronomic factors in soil and spike samples, and it was found that factors such as planting methods, irrigation conditions, and last season's straw treatment methods could affect corn. The type and quantity of plant-contaminated fungi resulted in differences in the levels of corn kernel mycotoxins.