Carbonaceous materials have proved to be effective in cadmium remediation, but their influences on soil microecology have not been studied well. Taking the structural differences and the maintenance of soil health as the entry point, we chose graphene (G), multi-walled carbon nanotubes (MWCNTs), and wetland plant-based biochar (ZBC) as natural and engineered carbonaceous materials to explore their effects on Cd fractions, nutrients, enzyme activities, and microbial communities in soils. The results showed that ZBC had stronger electronegativity and more oxygen-containing functional groups, which were related to its better performance in reducing soil acid-extractable cadmium (EX-Cd) among the three materials, with a reduction rate of 2.83–9.44%. Additionally, ZBC had greater positive effects in terms of improving soil properties, nutrients, and enzyme activities. Redundancy analysis and correlation analysis showed that ZBC could increase the content of organic matter and available potassium, enhance the activity of urease and sucrase, and regulate individual bacterial abundance, thereby reducing soil EX-Cd. Three carbonaceous materials could maintain the diversity of soil microorganisms and the stability of the microbial community structures to a certain extent, except for the high-dose application of ZBC. In conclusion, ZBC could better immobilize Cd and maintain soil health in a short period of time.