Rapid accumulation of soil lanthanum (La), cerium (Ce), and fluorine (F) caused by bastnasite mining development has increasingly become a concern worldwide in the past decades. However, the effects of the different chemical forms of these elements on the composition and diversity of soil dominant, moderate, and rare microorganisms are unclear. In this study, Planctomycetota was changed from dominant to moderate, caused by exchangeable and carbonate-bound forms of La and Ce. Both organic bound La (La_ORG) and water-soluble F (F_WS) were the crucial factors driving variations in the relative abundance of Patescibacteria and Bacteroidota from moderate to dominant, while the fungal phylum Chytridiomycota was changed from moderate to dominant, promoted by F_WS. La_ORG, the ferrum-manganese bound form of Ce, and F_WS displayed a negative correlation with the three rare bacterial phyla, i.e., Abditibacteriota, GAL15, and Deinococcota respectively. F_WS caused the disappearance of the rare fungal phylum Monoblepharomycota and the appearance of the rare bacterial phylum Fibrobacterota. Organic bound forms of both Ce and F showed a negative correlation with the bacterial Sobs and fungal Phylogenetic diversity indices, respectively. To summarize, the different chemical forms of La, Ce, and F showed varied effects on the composition and diversity of soil microbial communities.