Abstract: The microstructure of bone tissue is similar to that of fiber-reinforced composites. It mainly consists of the mineral and organic matters arranged alternately. Three kinds of collagen microfibril models were constructed based on the degree of mineralization. The effect of organic phase on mechanical properties of microfibril was investigated on considering of tropocollagen molecules and organic cross-links. The results were further studied by compared with the literature reported. The numerical results show that the stiffness value and trend of plastic deformation of the microfibril models are significantly improved with the increasing of the degree of mineralization. Shrinkage of tropocollagen molecules results in the increase of elastic modulus and the decrease of toughness. The mechanical properties of bone tissue improve and its brittleness increases with the increasing of the number of cross-links. The results are helpful to reveal the effects of the active constituents and microstructures of bone tissue on its mechanical properties, which can provide theoretical foundations to develop bone repair materials.