In the present study, we revealed that, in FLT3-ITD-positive AML, FLT3 inhibitor resistant cells overexpressed autophagy; Autophagy was activated by acquired D835Y mutation or BME and then mediated FLT3 inhibitor resistance; Autophagy activation reduced the suppression efficacy of FLT3 inhibitors on FLT3 downstream signaling and then decreased their pro-apoptotic effect; Inhibition of autophagy enhanced the anti-leukemia effect of FLT3 inhibitors, partly overcame FLT3 inhibitor resistance,. This evidence concerns the gene FLT3 and leukemia.