The origin of the near-infrared photoluminescence (PL) from thiolate-protected gold nanoclusters (Au NCs, <2 nm) has long been controversial, and the exact mechanism for the enhancement of quantum yield (QY) in many works remains elusive. Meanwhile, based upon the sole steady-state PL analysis, it is still a major challenge for researchers to map out a definitive relationship between the atomic structure and the PL property and understand how the Au(0) kernel and Au(I)-S surface contribute to the PL of Au NCs. Herein, we provide a paradigm study to address the above critical issues. By using a correlated series of "mono-cuboctahedral kernel" Au NCs and combined analyses of steady-state, temperature-dependence, femtosecond transient absorption, and Stark spectroscopy measurements, we have explicitly mapped out a kernel-origin mechanism and clearly elucidate the surface-structure effect, which establishes a definitive atomic-level structure-emission relationship. A ∼100-fold enhancement of QY is realized via suppression of two effects: (i) the ultrafast kernel relaxation and (ii) the surface vibrations. The new insights into the PL origin, QY enhancement, wavelength tunability, and structure-property relationship constitute a major step toward the fundamental understanding and structural-tailoring-based modulation and enhancement of PL from Au NCs.