Cronobacter spp. is an opportunistic pathogen that cause serious infections in all age groups. The organism has frequently been isolated from plant-based foods, especially cereals. Therefore, this study determined the occurrence, molecular characterization and tolerance of Cronobacter in fermented corn products (FCP) in China. Isolates were speciated and genotyped according to multilocus sequence typing (MLST), which included the pathogenicity associated allele ompA, as well as serotyping. Twenty-two strains of Cronobacter (20 C. sakazakii and 2 C. muytjensii) were isolated from 216 FCP samples, such as fermented corn noodles, fermented corn doughs, fermented corn vermicelli, fermented corn flour paste, fermented corn beverage, and fermented corn bread. All Cronobacter isolates were divided into 8 sequence types (STs), 4 serotypes and 4 ompA genotypes. The dominant type (10/22) was C. sakzakii ST8, C. sakazakii serotypes O:2, and ompA5, mainly in fermented corn noodle and fermented corn dough. Of all the strains, Cronobacter strains with ST770 had a stronger ability to tolerate acid, osmotic stress and cold, while Cronobacter strains with ST8 had a weaker tolerance to acid, osmotic stress and cold. Eight isolates exhibited strong biofilm-forming ability (OD595 > 1), among which the ST770, ST771, and ST556 strains showed more pronounced abilities. All Cronobacter isolates were sensitive to amoxicillin/clavulanic acid, ceftazidime, aztreonam, meropenem, tetracycline, ciprofloxacin, trimethoprim/sulfamethoxazole, polymyxin B, and chloramphenicol, while 77.27% of isolates were resistant to cefotaxime. This study supports the concern of Cronobacter transmission through plant-based foods, and provides a theoretical basis for the prevention and control of this pathogen in FCP.