Cadmium (Cd) pollution in soil pose a grave threat to human health. Combining various approaches to reduce Cd accumulation in crops is an active area of research to remediate farmlands with medium-high levels of Cd contamination. The Mercapto-functionalized palygorskite (PGS-SH) and zinc (Zn) application alone or in combination was investigated to explore reduction of Cd uptake in B. chinensis L and transformation of Cd in soil. The sole application of Zn or PGS-SH increased the biomass of B. chinensis L. and decreased the concentration of Cd in plants, but more improvements were observed from the combined application of Zn and PGS-SH. Low concentration of exogenous Zn (50 mg/kg) significantly increased the soil respiration rate (SRR) and the soil dehydrogenase activity (sDHA), while promoted B. chinensis L. growth while inhibiting Cd uptake. However, excessive exogenous Zn (≥ 200 mg/kg) significantly inhibited B. chinensis L. growth and soil microbial activity. The combined application of PGS-SH and Zn had the highest sDHA (145.59%) and lowest transport factor (TF) (27.59%) compared with the CK. The combination of PGS-SH and Zn fertilizer is a safe and effective means for remediating Cd-contaminated soil and restoring microbial activity.