We have used high-energy X-ray scattering to measure the structural anisotropy and excess free volume in a homogeneously deformed Zr-based metallic glass alloy. The scattering results show that bond length anisotropy is present in the samples following isothermal tensile creep deformation. The average atomic bond length in the direction parallel to the tensile loading axis is larger than that in the direction normal to the loading axis. The magnitude of the bond length anisotropy is found to be dependent on the gradient of macroscopic plastic strain along the gauge length. Furthermore, the scattering results show that the excess free volume also increases with increasing macroscopic plastic strain. Results from differential scanning calorimetry analysis of free volume variations along the gauge length of the creep samples are consistent with results from the X-ray scattering experiments.