Objective To study the effect of non-self-similar hierarchy on fracture mechanical properties and crack propagation of the biocomposite. Methods The numerical models were established by using ABAQUS, and the stiffness and crack initiation and propagation in the biocomposite with the inclination angles between the axis of the prism and mineralized collagen fibrils θ=0°,20°,40°,60°,80° were simulated by extended finite element method. Results The inclination angle θ had limited influences on biocomposite stiffness at θ≤40°, while biocomposite stiffness decreased with θ at θ>40°. The ultimate tensile strain also increased at θ>40°. Asymmetry in the crack was also found during propagation of matrix surrounded-enhanced phases at θ>0°. The crack propagatation on one side of the long axis of the mineral crystal was relatively easier than that on the other side at θ>0°. Conclusions The non-uniform distributions of cracks were found in biological hard tissues arisen from the non-self-similar hierarchy. The non-uniform crystal arrangement in the biocomposite would result in local damage rather than catastrophic fracture. The findings of this study can provide theoretical support for material design.