FLT3 protein kinase is a promising target for the treatment of acute myeloid leukemia (AML), and the development of this kinase inhibitor is highly desirable to overcome FLT3-positive AML. Herein, the bioactive predictions and screening were conducted based on our previous machine learning model in this work. Using ZY06 as a candidate, the design, synthesis and biological evaluation of a series of 4-(imidazo[1,2-a]pyridine-3‑carbonyl) phenyl urea derivatives as novel FLT3 inhibitors were systematically investigated. These compounds exhibited excellent inhibitory potency towards FLT3-ITD kinase, and moderate to potent antiproliferative activities against MV4-11 cells. The compound ZY12 displayed good selectivity to other kinases and excellent bioactivity in vitro, and concentration-dependently induced cycle arrest of MV4-11 cells. Moreover, ZY12 could significantly block the phosphorylation of FLT3 and its downstream signal pathways, such as AKT and ERK, and exhibit good safety in vivo, which serve as a lead molecule for developing novel FLT3 inhibitors against AML.