The Zr64.2Ni16.2Cu14.6Al5 and Zr63.4Ni16.2Cu15.4Al5 bulk amorphous alloys with heterogeneous structures were prepared through copper mould casting. The microstructures and thermal stabilities of two Zr-based bulk amorphous alloys were investigated by X-ray diffraction (XRD) and differential scanning calorimetry (DSC). Compared with homogenous structure Zr65A10lNi10Cu15 bulk amorphous alloys, heterogeneous structure decreases alloy thermal stability. The two Zr-based bulk amorphous alloys exhibit large plastic strain (>25%) and high yield strength (>1.6 GPa) under uniaxial compression tests. The low potential-energy barrier of shear transition zones (STZs) and the high resistance of the shear bands propagation are regarded as the main reason of increasing of plasticity in the bulk amorphous alloy with heterostructure.