Hat-shaped beams played an important role in the body load-bearing structure, such as B-pillar. Fiber metal laminates possessed great advantages of excellent stiffness/strength, high damage tolerance and lightweight effect. In order to improve the catastrophic damage mode of carbon fiber, the hat-shape thin-walled hybrid beams consisting of carbon fiber reinforced thermoplastic (CFRP) prepreg and aluminum (Al) sheet were proposed and fabricated by hot-pressing molding. The effects of carbon fiber layer numbers, CFRP/Al stacking sequence, and the CFRP layup orientation on the three-point bending performance and failure mode of the hat-shaped hybrid beams were investigated. The results showed that the more CFRP layer, the better the bending performance of the hybrid hat-shaped beams. The CA-2 hat-shaped beams generated overall lateral deformation. The ACA (Al/CFRP/Al) hat-shaped beams achieved a higher CFE (ratio of average load to peak force) value and better energy absorption effect. The deformation processes of AC (Al/CFRP) and ACA stacking structures was similar, the horizontal web concave and the side walls on both sides convex. In terms of fiber lay-up orientation, ACA-OR (orthogonal) possessed superior bending performance and energy absorption to the ACA-UD (unidirectional) hybrid beams. Furthermore, the failure mechanism of the ACA hybrid beams was analyzed and the cross-sectional microstructure at different sections were observed by SEM. Matrix cracking, interfacial delamination, fiber fracture and metal plastic deformation were detected, which played a supporting effect and energy absorption role.