The variations in material composition, phase and structure can provide a useful tool for tuning emission colour, but the controlling of the emission colour in a material, with a composition fixed, remains to be a daunting challenge. In this work, we systematically study the luminescence selective output characteristics of Tm3+ doped NaYF4 nanorods, and also the dependences of fluerecence output on pulse duration, excitation wavelength, pump power, and ambient temperature. The results show that the color of output light is strongly dependent on laser pulse duration compared with other factors. The temperature dependent luminescence of the nanorods shows very different behaviors with short-pulse laser excitation from those of continuous wave (CW) laser. When the pulse laser at 656 nm is employed, the emission spectra from NaYF4:0.5 mol% Tm3+ nanorods at the different temperatures are dominated by near-infrared (NIR) luminescence about 800 nm accompanied with weak blue luminescence, giving rise to nearly spectrally-pure NIR emissions at 20 K. When the pulse laser is replaced by CW laser, blue double emissions at 453 and 478 nm with the same order of magnitude of NIR luminescence can be clearly detected at room temperature. The key mechanism responsible for colour-tunable emission can be explained in terms of the population process of luminescence level, in which the different luminescence level populations need different time intervals. Considering excited-state absorption (ESA) for a particular 1D2 energy level, there needs an extra step of 3F2, 33H4 multiphonon nonradiation relaxation process to populate the 3H4 state and subsequently pump its 1D2 state for blue emission. Therefore, the pulse width should be longer than nonradiation relaxation time of 3F2, 33H4 to comply with the ESA, while the nonradiation relaxation time can further be tuned by controlling ambient temperature. We show that the variation of the excitation power leads to interesting change in the upconversion (UC) decay curve. We focus our attention on the excitation wavelength dependences of 3H4 and 1D2 emission lifetimes in order to validate the population mechanism of luminescence level. We demonstrate that the 3H4 luminescence time depends on excitation wavelength, while 1D2 emission lifetime nearly keeps constant when varying the excitation wavelength. Based on multi-phonon relaxation theory and time-resolved photoluminescence studies, it is indicated that the UC luminescence under short-pulse laser excitation mainly originates from the ions at/near the surface, while downconversion is mainly from the ions in the core for NaYF4:Tm3+ nanorods. The single-band NIR luminescence output by changing the pulse width and excitation wavelength provides an insight into the controlling of the population processes of luminescent levels and offers a versatile approach to tuning the spectral output.