This study aimed to assess the effectiveness of combining phytoextraction and biochar for metal-polluted wetland soils by exploring the changes in soil biochemical properties, especially compared to the outcomes of single phytoremediation or biochar application. Soil biochemical properties serve as reliable indicators of soil quality and exhibit a high sensitivity to microbial community dynamics. Phytoextraction is via the native plants Phragmites australis (P. australis) and Suaeda salsa (S. salsa). The addition of biochar significantly increased the total organic carbon (TOC) and available potassium (AK) contents in the rhizosphere soil of P. australis and more in that of S. salsa. The effects of the combined remediation on the composition of the main classes of bacteria are uncertain, and the abundance of the main fungal classes decreased. At the level of OTU, no significant differences were observed in the richness and diversity of microbial communities between the single and combined remediation approaches. On a genus level, the combined remediation of biochar and S. salsa had the highest specificity of soil bacteria, while the single biochar remediation gave the highest specificity of soil fungi. At the class level, the four most abundant classes of bacteria were actinobacteria, alphaproteobacteria, gammaproteobacteria, and bacterricilineae. Biochar addition decreased the abundance of actinobacteria in P. australis rhizosphere soil but increased the abundance of actinobacteria in S. salsa rhizosphere soil. The sordariomycetes and eurotiomycetes were the dominant fungal classes. The combined remediation reduced the abundance of sordariomycetes, and the abundance of eurotiomycetes decreased after single phytoextraction, biochar, and combined remediation.