Petroleum pollution in desert regions is a severe environmental issue arising from petroleum industry activities. N-hexadecane, a common long-chain alkane found in petroleum products, is chemically stable and resistant to degradation. This study aims to investigate the degradation efficiency of n-hexadecane in desert soil by Rhodococcus erythropolis KB1 and its regulatory effect on the structure of the indigenous microbial community. Through microcosm experiments comparing natural degradation and bioaugmentation remediation, it was found that, over a 49-day incubation period, the inoculation KB1 significantly increased n-hexadecane degradation rates from 42.87% in the natural degradation group to 54.13%. In sterilized soil systems, KB1 achieved a degradation rate of 60.90% when used alone, confirming its inherent high degradation capacity. Further microbial community analysis revealed that bioremediation significantly altered soil microbial structure. At the phylum level, the relative abundance of Actinobacteria increased to 30.23%, making it the dominant phylum. At the genus level, Rhodococcus increased to 16.58%, accompanied by the synergistic enrichment of functional groups such as Nocardioides and Ohtaekwangia. This study demonstrates that R. erythropolis strain KB1 not only directly degrades n-hexadecane but, as indicated by bioinformatics analyses, also enhances synergistic remediation functions at the community level by modulating the indigenous microbiome. This study provides a theoretical foundation and microbial resources for desert oil pollution remediation based on bioremediation technology.