Antimicrobials may be used to inhibit the growth of micro-organisms in the cultivation of mung bean sprouts, but the effects on mung bean sprouts are unclear. In the present study, the growth performance, morphology, antimicrobial effect and antimicrobial residues of mung bean sprouts cultivated in typical antimicrobial solutions were investigated. A screening of antimicrobial residues in thick-bud and rootless mung bean sprouts from local markets showed that the positive ratios of chloramphenicol, enrofloxacin, and furazolidone were 2.78%, 22.22%, and 13.89%, respectively. The cultivating experiment indicated that the production of mung bean sprouts in antimicrobial groups was significantly reduced over 96 h (p < 0.05). The bud and root length of mung bean sprouts in enrofloxacin, olaquindox, doxycycline and furazolidone groups were significantly shortened (p < 0.05), which cultivated thick-bud and rootless mung bean sprouts similar to the 6-benzyl-adenine group. Furthermore, linear regression analysis showed average optical density of 450 nm in circulating water and average production had no obvious correlation in mung bean sprouts (p > 0.05). Antimicrobial residues were found in both mung bean sprouts and circulating water. These novel findings reveal that the antimicrobials could cultivate thick-bud and rootless mung bean sprouts due to their toxicity. This study also proposed a new question regarding the abuse of antimicrobials in fast-growing vegetables, which could be a potential food safety issue.