The atomic configuration of chemical short-range order (CSRO) for the Zr-base metallic glasses was investigated by using nano-diffraction and high resolution transmission electronic microscopy (HRTEM) technology with a beam size of 0.5 nm. It is illustrated that the pattern of atomic configuration of CSRO might have various compound counterparts because of the chemical interaction of bonding atoms. Some atomic configuration of MCSRO is similar to the icosahedral structure with 10-fold symmetry of very weak spots. In deed, the nano-beam technology could clearly detect the evolution of atomic configuration in nanometer scale during the transformation from the metallic melt to the primary crystallization. The local atomic configuration of CSRO is also investigated by molecular dynamics simulation (MD) for the Zr2Ni compound in a wider temperature range. The CSRO in the melt could be pictorially demonstrated as distorted coordination polyhedron of the compound structure and/or the structure similar to cubo-octahedron analogs. The MD simulation illustrates that the atomic packing of long-range order disappears just above the melting point, but the chemical interaction of bonding atoms still exists that leads to form the various CSRO with the atomic configuration similar to stable or metastable unit cell of Zr2Ni compound. The icosahedral polyhedron became more abundance as the overheating temperature was raised.