Synthesis of lanthanide-doped upconversion nanocrystals (LDUNs) with controlled morphology and luminescence has long been desired in order to fulfill various application requirements. In this work, we have investigated the effect of the NaF : Ln(3+) molar ratio, in the range of 1 to 20, on the morphology, crystal structure, and upconversion properties of NaxScF(3+x):Yb/Er nanocrystals that are reported to possess different upconversion properties from those of NaYF4:Yb/Er nanocrystals. The experimental results prove that the NaF : Ln(3+) molar ratio influences significantly the growth process of the nanocrystals, i.e. a low NaF : Ln(3+) molar ratio results in hexagonal NaScF4 nanocrystals, while a high NaF : Ln(3+) molar ratio favors monoclinic Na3ScF6 nanocrystals. When the NaF : Ln(3+) molar ratio is as high as 6 or above, phase separation is found and hexagonal NaYbF4 nanocrystals showed up for the first time. Simply by adjusting the NaF : Ln(3+) molar ratio, we have successfully achieved the simultaneous control of the shape, size, as well as the crystallographic phase of the NaxScF(3+x):Yb/Er nanocrystals, which give different red to green (R/G) ratios (integral area), leading to a multicolor upconversion luminescence from orange-red to green. This study provides a vivid example to track and interpret the formation mechanisms and growth processes of NaxScF(3+x):Yb/Er nanocrystals, which shall be instructive for guiding the controlled synthesis of other LDUNs and extending their according applications in optical communication, color display, anti-counterfeiting, bioimaging, and so on.