Nanoparticle films sputtered on substrates are key building blocks for photovoltaics, chemical/biological sensors, portable/wearable devices, magnetic devices, and catalysis. For these applications, high size and shape uniformities are highly demanded for improving their functional performance. However, flat substrate surface generally leads to unsatisfied size and shape uniformities. Here, a universal and sputtering rate-tolerant strategy for improving the uniformities by introducing densely spaced nanoprotrusions (NPTs) at substrate surface is proposed. Unlike the conventional flat surface where the thermodynamic processes are substantially random, the NPTs can predefine the nucleation sites and confine the diffusion of sputtered atoms on the top, and eventually enable uniform nucleation and growth of nanoparticles. The morphological and surface plasmon spectroscopic analyses disclose that the size and particle shape uniformities of the sputtered nanoparticles are significantly improved by this strategy. Finally, an unprecedented universality and high tolerance to sputtering rate of the approach are confirmed by extending the approach to other material systems. Because of the simplicity of the working mechanism, the proposed strategy is expected to be readily extended to more material systems for applications.