In this study, we attempt to identify the presence of surface defects (SDs) at an n-type GaN surface after high-temperature growth and gain insight into their intrinsic features. To this end, first, we carefully investigate n-type GaN samples with different surface etching depths. Low-temperature photoluminescence (PL) spectra reveal that SDs are most likely nitrogen vacancies (VN) and/or VN-related point defects intensively distributed within ∼100 nm from the n-type GaN surface after a high-temperature growth. We investigate the effect of SDs on the internal quantum efficiency (IQE) of green light-emitting diodes (LEDs) by preparing GaInN-based green LEDs employing a surface-etched n-type GaN, which exhibits a prominent enhancement of the PL efficiency with an increase in the etching depth. This effect is attributable to the reduced non-radiative recombination centers in multiple-quantum-well active regions because the SDs near the n-type GaN surface are removed by etching. We discuss strategies of in situ engineering on SDs to further improve the IQE in GaInN-based green LEDs on the basis of the results presented in this study.