Recently, lanthanide based nanocrystals with upconversion fluorescence emission have attracted a lot of interest and the nanocrystals have been used for bioimaging, biodetection, and therapeutic applications. Use of the nanocrystals for multiplexed detection has also been explored; however, nanouystals with multicolor emission are required. Some efforts have been made to tune the emission spectra of the nanocrystals based on manipulation of upconverting lanthanide ions doped in the crystals or creation of core/shell structures. In this work, alkali ions with an ionic radius slightly larger or smaller than Na such as Li and K were doped into NaYF4:Yb,Er nanocrystals and their effect on the crystal structure and subsequently the upconversion emission spectra were studied. It was found that the phase transition occurs in the nanocrystals when a different amount of Li and K was doped. Furthermore, the intensity ratios between the blue, green, and red emission peaks changed accordingly, and make it possible to tune the upconversion fluorescence of the nanocrystals by Li and K doping.