A semiconductor substrate, a semiconductor device and a manufacturing method of the semiconductor substrate are provided. The semiconductor substrate comprises a first semiconductor layer and a second semiconductor layer located on the first semiconductor layer. The first semiconductor layer and the second semiconductor layer, as well as semiconductor layers obtained by symmetrically rotating the first semiconductor layer and the second semiconductor layer according to their respective lattice structures, have different cleavage planes in a vertical direction. By providing the semiconductor substrates having composite structures, even if thicknesses of the substrates are not changed, the damages to the semiconductor substrates due to stresses by the semiconductor epitaxial layers can be reduced, thereby decreasing the likelihood of breakage of the semiconductor substrates. Furthermore, the processing difficulty is reduced and the reliability of the semiconductor devices is improved.