Optical biomedical imaging using luminescent nanoparticles as contrast agents prefers small size, as they can be used at high dosages and efficiently cleared from body. Reducing nanoparticle size is critical for the stability and specificity for the fluorescence nanoparticles probes for in vitro diagnostics and subcellular imaging. The development of smaller and brighter upconversion nanoparticles (UCNPs) is accordingly a goal for complex imaging in bioenvironments. At present, however, small UCNPs are reported to exhibit less emission intensity due to increased surface deactivation and decreased number of dopants. Here we show that smaller and more efficient UCNPs can be made by improving the interior crystal quality via controlling heating rate during synthesis. We further developed a unique quantitative method for optical characterizations on the single UCNPs with varied sizes and the corresponding shell passivated UCNPs, confirming that the internal crystal quality dominates the relative emission efficiency of the UCNPs.