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Abstract Lanthanide-doped upconversion nanomaterials are emerging as promising candidates in optoelectronics, volumetric display, anti-counterfeiting as well as biological imaging and therapy. Typical modulations of upconversion through chemical methods, such as controlling phase, composition, morphology and size enable us to rationally manipulate emission profiles and lifetimes of lanthanide ions by using continuous-wave laser excitation. Here we demonstrate that under pulsed laser excitation the emission color of NaYF4:Er/Tm (2/0.5%)@NaYF4 core-shell nanoparticles has an obvious transformation from green to red colors. Moreover, both pulse duration and repetition frequency are responsible for manipulating the upconversion emission color. The mechanism of the phenomena may be that the pulsed laser sequence triggers the emission levels to non-steady upconversion states first, and then cuts off the unfinished population process within the pulse duration. This pump source dependent and resultant tunable fluorescence emission enables NaYF4:Er/Tm (2/0.5%)@NaYF4 nanoparticles as a promising fluorophore in the transparent anti-fake printing.