Three-dimensional braided composite has a unique spatial network structure that exhibits the characteristics of high delamination resistance, damage tolerance, and shear strength. Considering the characteristics of braided structures, two types of high-performance materials, namely, aramid and carbon fibers, were used as reinforcements to prepare braided composites with different hybrid structures. In this study, the longitudinal and transverse shear properties of 3D braided hybrid composites were tested to investigate the influences of hybrid and structural effects. The damage characteristics of 3D braided hybrid composites under short beam shear loading underwent comprehensive morphological analysis via optical microscopy, water-logging ultrasonic scanning, and X-ray micro-computed tomography methods. It is shown that the shear toughness of hybrid braided composite has been improved at certain degrees compared with the pure carbon fiber composite under both transverse and longitudinal directions. The hybrid braided composites with aramid fiber as axial yarn and carbon fiber as braiding yarn exhibited the best shear toughness under transverse shear loading. Meanwhile, the composites with carbon fiber as axial yarn and aramid fiber as braiding yarn demonstrated the best shear toughness in the longitudinal direction. Due to the different distribution of axial and braiding yarns, the transverse shear property of hybrid braided structure excels over the longitudinal shear property. The failure modes of the hybrid braided composite under the two loading directions are considerably different. Under transverse loading, the primary failure mode of the composites is yarn fracture. Under longitudinal loading, the primary failure modes are resin fracture and fiber slip. The extensive interfacial effects and the good deformation capability of the hybrid braided composites can effectively prevent the longitudinal development of internal cracks in the pattern, improving the shear properties of braided composites.