Abstract: To investigate the effects of potato and maize compound planting on allelochemicals accumulation and bacterial community structure, soil samples from continuous potato cropping, continuous maize cropping, potato and maize intercropping, and potato-maize rotation were collected in the eighth year of the experiment. Allelochemicals extracted from the soil were determined by GC-MS. Then, Illumina Miseq high-throughput sequencing technology was used to sequence the 16Sr DNA V4-V5 regions of soil bacteria to analyze changes in soil bacterial diversity and community structure. The results showed that:1) continuous cropping of maize and potatoes led to the accumulation of allelochemicals, 2) continuous maize cropping caused soil to accumulate more fatty acids such as oleic acid, linoleic acid, eicosanoic acid, and lignoceric acid, and 3) potato continuous cropping produced soil with more accumulated fatty alcohols such as 1-octadecanol and 1-eicosanol. Rotation reduced the accumulation of most allelochemicals, and the number of allelochemicals that were reduced by intercropping was smaller than that by rotation. The soil bacteria community structure changed significantly among different planting patterns. Compared with continuous cropping, intercropping and rotation had higher Ace and Chao indices. At the phylum level, the abundance of Actinobacteria was significantly higher under rotation than under continuous cropping of potato, the abundance of Bacteroides was significantly lower under intercropping than under continuous cropping of maize, and the abundance of Acidobacteria was significantly higher under both potato and maize continuous cropping than under rotation cropping. At the genus level, some beneficial bacteria such as Arthrobacter and Lysobacteria were relatively more abundant in compound planting soils. Through correlation analysis, it was found that the abundances of Pedomicrobium and Pirellula genera were significantly positively correlated with fatty alcohols, and that of Flavobacterium, Lysobacteria, and Microbacteria genera were significantly negatively correlated with fatty acids. Compound planting of potato and maize reduced the accumulation of allelochemicals in the soil, thus inhibiting reduction in soil bacterial abundance, increasing the abundance of beneficial bacteria, and ameliorating the issues associated with continuous cropping.