In this paper, the microstructural characteristics and mechanical behavior of 2D C/SiC two-layer beams with pin-bonded hybrid joints were investigated. The pin joints were incorporated into the two-layer beam during the assembling stage, and the adhesively bonded joints can be introduced by subsequent chemical vapor infiltration (CVI) process. For 2D C/SiC two-layer beam it was confirmed that the distribution of the adhesively bonded joints was random. Based on the partial interaction composite beam theory, a simplified method was proposed to characterize the effect of adhesively bonded joints on the bending stiffness of the 2D C/SiC two-layer beam. The stress distribution around the pin joints was described by finite element modeling. It was found that the radial stress, the hoop stress and the in-plane shear stress around the pin joints were unique in their distributions. Under the action of these stresses, two kinds of failure modes can be initiated: one is the debonding of the pin–hole interface, and the other is the fracture of the 2D C/SiC plate. Based on the stress results, an empirical failure criterion was present to predict the ultimate failure of the 2D C/SiC two-layer beam.