[Background] Jinsha earthen site is considered as a large ritual site in the Shang and Zhou dynasties 3 200 years ago, which play an important role in ancient culture and history. But now it has exhibited different degrees of degradation under the influence of physical, chemical and biological factors. The effects of physical and chemical factors have been reported, while very little is known about the influence of biological factors on earthen site. [Objective] To study the microbial diversity and metabolic characteristics in Jinsha earthen site soil, it is important to provide scientific evidences for the conservation of Jinsha earthen site. [Methods] Four types of representative samples from Jinsha earthen site that have undergone different degree of degradation were collected to analyze the microbial diversity and metabolic function by Biolog plate methods and denaturing gradient gel electrophoresis (PCR-DGGE). The degree of degradation of samples is followed by J4>J3>J2>J1. [Results] Biolog analysis result showed that the function of soil microbial diversity was significantly varied in different samples and the order of microbial metabolic activity was followed by J2>J3>J4>J1, implying that the microbial metabolic activity of samples showed an increasing trend with the degradation of soil. PCA analysis of Biolog indicated the utilized types of carbon sources by soil microbes in Jinsha earthen site was significantly varied. The microorganisms in sample J2 could utilize most types of substrate carbon sources in plate compared to that in other samples, and the preferred carbon sources of sample J2 was obviously different from that of other samples. The bacterial diversity and structure of different soil exhibited significant difference by DGGE analysis. The order of microbial community diversity was followed by J2>J4>J3>J1 both in DNA and RNA level and the PCA result of DGGE revealed that the total and active bacterial community showed high consistency except sample J1, which indicated the microbial diversity increased with the degradation of soil. Based on the sequence analysis of DGGE, the major community of bacteria in soil samples were belonged to Actinobacteria, Acidobacteria, Proteobacteria and Deinococcus-Thermus. Rubrobacter and Brevundimonas were detected in all samples, including DNA and RNA level. [Conclusion] It is first time that microbial and functional diversity of soil from Jinsha earthen site were analyzed in this study. The results exhibited the microbial and functional diversity increased with the degradation of soil. The genera Rubrobacter, Tellurimicrobium and Brachybacterium that were detected only in degraded soil samples or had high expression activity may be involved in the soil degradation process. The results could provide theoretical basis for the scientific conservation of Jinsha earthen site.