In this study, the out-of-plane shear strength of hybrid cross-laminated timber (CLT) with outer layers of hinoki (hinoki cypress, Chamaecyparis obtusa) and inner layers of sugi (Japanese cedar, Cryptomeria japonica) is investigated for four different layer configurations. To investigate the influence from rolling shear properties of cross layers on the shear strength of CLT, stress analysis was conducted using the shear analogy method. The nominal shear strength, the maximum shear force divided by the cross-section of CLT, was in the 1.0–2.1 MPa range. Using the shear analogy method, the rolling shear modulus in the cross layer was determined as 72.9 MPa, which was comparable with the value obtained for laminae in previous study as well as the value confirmed by strain measurements in the present study. The magnitude of rolling shear stress in the cross layer was 0.9–1.1 times the average shear stress, which was negatively correlated with the nominal shear strength. From the regression line between the nominal shear strength and the magnitude of the shear stress in the cross layer, the mean shear strength of the cross layer was estimated to be 1.33 MPa.