Abstract: Comprehending the pressure-/temperature-induced structural transition in glasses, as one of the most fascinating issues in material science, is far from being well understood. Here, we report novel polyamorphic transitions in a Cu-based metallic glass (MG) with apparent nanoscale structural heterogeneity relating to proper Y addition. The low-density MG compresses continuously with increasing pressure, and then a compression plateau appears after 8.1 GPa, evolving into an intermediate state with an ultrahigh bulk modulus of 467 GPa. It then transforms to a high-density MG with significantly decreased structural heterogeneity above 14.1 GPa. Three-dimensional atom probe tomography reveals concentration waves of Cu/Zr elements with an average wavelength of 5-6 nm, which promote the formation of interconnected ringlike networks composed of Cu-rich and Zr-rich dual-glass domains at nanometer scale. Our experimental and simulation results indicate that steplike polyamorphism may stem from synergic effects of the abnormal compression of the Zr-Zr bond length at the atomic scale and the interplay between the applied pressure and incipient concentration waves (Cu and Zr) at several nanometer scales. The present work provides new insights into polyamorphism in glasses and contributes to the development of high-performance amorphous materials by high-pressure nanostructure engineering.