The microRNAs (miRNAs) of their hosts play an important role in regulating both the innate and adaptive immune responses to
Cryptosporidium parvum
infection. The mechanisms of autophagy and apoptosis are important components of the defense system against
C. parvum
infection. In this study, we investigate the role of miRNA-199a-3p in regulating MTOR-mediated autophagy and apoptosis in HCT-8 cells induced by
C. parvum
. The expression of miR-199a-3p increased at 3, 6 and 12 hours postinfection (hpi) but decreased at 24 and 48 hpi. The upregulation of miR-199a-3p promoted autophagy and apoptosis and limited the parasite burden in HCT-8 cells after
C. parvum
infection. The downregulation of miR-199a-3p inhibited the autophagy and apoptosis induced by
C. parvum
and enhanced the parasite burden in HCT-8 cells. A luciferase reporter showed that MTOR was a target gene of miR-199a-3p. Suppressed expression of MTOR by small interfering RNA (siRNA) promoted autophagy and apoptosis and limited
C. parvum
burden in HCT-8 cells. Co-transfection with miR-199a-3p inhibitor or si-mTOR revealed that miR-199a-3p regulates autophagy and apoptosis in HCT-8 cells through MTOR, to resist
C. parvum
infection. In conclusion, intestinal epithelial cells defend against
C. parvum
infection by regulating their autophagy and apoptosis through the miR-199a-3p-MTOR axis.