In this work, the uniform bundle-shaped microtubes composed of six half-pipes are synthesized for the first time in hydrothermal solutions via an intentional delayed phase transition pathway induced by Mn(2+) doping. The structural and kinetic factors that govern the phase and shape evolution of NaYF4 microcrystals have been carefully studied, and the influences of Mn(2+) to RE(3+) ratio, the amount of trisodium citrate, and the pH value in conjunction with the intrinsic character of RE(3+) ions on the phase and shape evolution are systematically discussed. It is found that the proper Mn(2+) to RE(3+) ratio is mainly responsible for delayed phase transition process and induces interior density gradient of solid aggregate for creating hollow bundle-shaped microtubes. While the amount of trisodium citrate and the pH value are the keys for the shape control of the NaYF4 microcrystals such as prismatic microtubes, prismatic short rods, thin plates, and particles. The up and downconversion emissions were obtained independent of whether α- or β-NaYF4:Er(3+)/Yb(3+) samples doped with Mn(2+), but the significant tuning of output color was only obtained in cube NaYF4 nanoparticles rather than in hexagonal microtubes via adjusting the amount of Mn(2+) ions. These spectral measurements and EDX analyses indicate that the distribution or concentration of Mn(2+) in hexagonal phase solid solution has changed, which supports Ostwald ripening growth mechanism and rules out agglomeration or oriented attachment growth mechanism. We designed crystal growth mode by simply addition of dopant may provide a versatile approach for fabricating a wide range of hollow nano/microcrystals and thus bring us a clearer understanding on the interaction between the dopant reagents and the nano/microcrystals.