We exploited a simple hydrothermal route without adding organic additives or hard templates to synthesize cubic-shaped LiNbO3:Yb3+/Er3+ with the size of 400–500 nm. Based on the time-dependent investigation on the crystal structure and morphology, Yb(NO3)3 and Er(NO3)3 not only could emit green and red upconversion (UC) emission but also could be used as an etchant to increase dissolution rate of the Nb2O5 raw material in the hydrothermal synthesis route. Without addition of Yb3+/Er3+ ions, LiNbO3 phase could not be formed at even hydrothermal time of 48 h. The time-dependent Raman spectra showed the Raman peaks of LiNbO3 were occurred at the reaction time of 48 h, and the impurity Nb2O5 phase was disappeared with lengthening hydrothermal time. After calcining at 1050 °C for 2 h, the new Raman peaks at 440/487/531/552 cm−1 and the disappeared OH– absorption peaks at 3429 and 1628 cm−1 favored to produce the bright UC emissions in LiNbO3:Yb3+/Er3+ nanocrystals. The pump power dependence and UC mechanism were studied under 980 nm excitation.