Atmospheric deposition of heavy metals such as Cd is a threat to ecosystems and food safety. Our knowledge is still limited about the effectiveness of remediation process for Cd-contaminated agro-soils under atmospheric Cd deposition. In this study, eight soil amendments were used in a Cd-contaminated purple soil to investigate their impacts on soil Cd availability, microbial response, and Cd uptake by mustard and corn plants via simulating the atmospheric Cd deposition under laboratory incubation and greenhouse conditions. Results showed that the simulated atmospheric Cd deposition increased the soil high-risk Cd (HR, exchangeable and carbonate Cd) and decreased soil medium-risk Cd fraction (MR, bound to Fe/Mn oxide and organic Cd), and the largest direct effects on crop Cd uptakes were 0.94 and 0.66 for mustard and corn based on the path-coefficient analysis, respectively. Generally, Cd deposition led to decreasing soil microbial biomass carbon, populations of bacteria, fungi and actinomycetes, and enzyme activities of urease, catalase, sucrase, and acid phosphatase whereas increasing soil microbial biomass nitrogen. Compared with control and lime treatments, an organic-inorganic combined preparation (OCP) appeared to be effective for remediation of the Cd-contaminated purple soil due to its potential to increase the HR-Cd and reduce both MR-Cd and crop Cd uptake, as accompanied by its neutral effects on soil bacterial alpha diversity and community structure. Results also indicated that application of nitrogen fertilizers should be considered for remediation of the Cd-contaminated soils as nitrogen inputs were demonstrated to promote soil health under elevated Cd condition. Display omitted •Atmospheric Cd deposition was explored firstly in Cd-contaminated soil remediation.•Direct effects of deposited Cd on Cd uptakes of mustard and corn were quantified.•Optimum amendment was made for Cd-contaminated purple soil exposed to Cd deposition.•Different responses of soil microbiome to simulated Cd deposition.•Nitrogen fertilizer should be considered during the Cd-contaminated soil remediation.