We demonstrate for the first time a new mechanical annealing method that can significantly improve the structural quality of self-assembled nanoparticle arrays by eliminating defects at room temperature. Using in situ high-pressure small-angle X-ray scattering, we show that deformation of nanoparticle assembly in the presence of gigapascal level stress rebalances interparticle forces within nanoparticle arrays and transforms the nanoparticle film from an amorphous assembly with defects into a quasi-single crystalline superstructure. Our results show that the existence of the hydrostatic pressure field makes the transformation both thermodynamically and kinetically possible/favorable, thus providing new insight for nanoparticle self-assembly and integration with enhanced mechanical performance.