Here, hydro/solvent thermal method was applied to synthesize lanthanide doped NaYF4 upconversion nanoparticles (UCNPs). In order to overcome the quenching effect of (CH2)n due to their high energy stretching vibration, a series of new chelating ligands such as, butanoic acid, hexanoic acid, decanoic acid, and tetradecanoic acid were selected for hydrothermal synthesis of NaYF4:Yb, Er nanocrystals. For comparison, commonly used oleic acid was also used as ligand for hydrothermal synthesis of UCNPs. The effect of the carbon chain length of chelating ligands on the NaYF4 nanocrystals’ emission intensity was systematically investigated. It was found that relative short length of the carbon chain in chelating ligands resulted in enhancement of luminescent intensity and modulation of the ratios of green to red (RGR) of NaYF4:Yb, Er nanocrystals. In contrast to the product prepared with oleic acid as ligand, the enhancement factors of 540nm emissions were 25, 21, 6.5, and 3 for samples prepared with butanoic acid, hexanoic acid, decanoic acid, and tetradecanoic acid as ligands, respectively. The FT-IR spectra of NaYF4:Yb, Er UCNPs prepared with different ligands indicated that ligands with relatively short chain length indeed have weak IR absorption in 2800–2950cm−1, which resulted in weak quenching effect of Er3+. We also synthesized NaYF4:Yb, Tm UCNPs with these ligands. The results showed that chain length of ligands has similar effect on emission intensity of NaYF4:Yb, Tm. It is expected that this method can also be applied to enhance the luminescence intensity of other luminescent materials.