A novel aqueous-based and phase-selected synthetic strategy toward YPO4:Ln(3+) (Ln = Ce, Eu, Tb) micro/nanocrystals was developed by selecting specific precursors whose structure topotactically matches with the target ones. It was found that layered yttrium hydroxide (LYH) induced the formation of hexagonal-phased h-YPO4.0.8H(2)O with the crystalline relationship of [001]LYH//[0001]h-YPO4.0.8H(2)O, while the amorphous Y(OH)CO3 favored the formation of tetragonal-phased t-YPO4. We also systematically investigated the influence of Na2CO3/NaH2PO4 feeding ratio on the evolutions of morphology and size of the h-YPO4.0.8H(2)O sample, and we also obtained a novel mesoporous nanostructure for t-YPO4 single crystalline with closed octahedron shape for the first time. Besides, the multicolor and phase-dependent luminescence properties of the as-obtained h-YPO4.0.8H(2)O and t-YPO4 micro/nanocrystals were also investigated in detail. Our work may provide some new guidance in synthesis of nanocrystals with target phase structure by rational selection of precursor with topotactic structural matching.