In this study, 183 sweet and waxy maize inbred lines were subjected to analyze the flowering time (Days to anthesis, DA), silking time (Days to silking, DS) and Anthesis silking interval (ASI) under Cd-polluted environments, in order to reveal the response and possible regulatory genes at the flowering stage. The results showed that Cd pollution prolonged DA and DS of sweet and waxy maize, especially for DS, which led to the increasing of ASI. The ASI value of waxy maize was found to be lower than that of sweet maize, implying the sensitivity of sweet corn under Cd stress. Three and six SNPs, which were associated with flowering time and silking time, respectively, were detected by Genome-wide association analysis (GWAS). These SNPs were found to be associated with eight genes annotated in maize GDB and NCBI gene databases, including few genes which were reported roles in the flowering time. Collectively, these results might provide theoretical reference for molecular marker assisted breeding and Cd safe breeding of sweet and waxy maize varieties in the future.