In this study, the effects of pollution levels and heavy metal pollution on soil microbial diversity in karst tea plantations are reported. Four tea plantations from plateau hills, under forests, by lakesides and on steep slopes in the South China karst were used as research regions. Soil samples were taken from these tea plantations, the soil heavy metals Cd, Cr, Pb, Zn, Ni and Cu were tested using inductively coupled plasma-mass spectrometry, and Hg and As were tested via atomic fluorescence spectrometry. The soil microbes were analyzed via high-throughput sequencing technology. Heavy metal pollution was evaluated via the single factor index and pollution load index, and the correlation between soil heavy metals and the microbial community was analyzed via SPSS 18.0 and Canoco 5.0 software. The results showed that the studied tea plantation soils were greatly polluted by the heavy metals, Cd and Hg, to a low to moderate degree. The comprehensive pollution of multiple heavy metals occurred only in lakeside tea plantations, in which pollution reached a low degree. It is also suggested that Hg and Cd were the major contributors, followed by Cu. The soil microbial diversity in soil samples from lakeside tea plantations was the highest; however, the discrepancy in its dominant species composition was also the highest. When the pollution load index was close to 0.6, the microbial diversity decreased sharply. Afterward, the diversity and heterogeneity generally gently increased, and the dominant composition was more obvious. These results reveal that the impact of heavy metal pollution on soil microbial diversity was not very distinct, but the impact on the dominant microbial community composition was obvious. In addition, the heavy metals, Cd, Hg and Cu, were the key factors that impacted the soil microbial community composition.