Ytterbium fluoride compounds with different crystal phases and morphologies, such as β-NaYbF4 hexagonal microdisks, microprisms, microtubes, and α-NaYbF4 submicrospheres as well as YbF3 octahedra, have been synthesized via a facile hydrothermal route. X-Ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM), selected area electron diffraction (SAED) and photoluminescence (PL) spectra were used to characterize the samples. The intrinsic structural feature of ytterbium fluoride compounds and four external factors, namely the pH values in the initial reaction solution, the fluoride source, the use of an organic additive (Cit3−) and simple ions (Na+, NH4+, BF4−, BO3−), are responsible for the ultimate shape evolutions of the products. The possible formation mechanisms for products with various architectures are presented. Additionally, the upconversion (UC) photoluminescence properties of β-NaYbF4:Er3+ hexagonal microdisks, microtubes, α-NaYbF4 spheres and YbF3 octahedra were investigated in detail. To the best of our knowledge, this is the first report concerning controllable synthesis of ytterbium fluoride compounds with diverse crystal phases and morphologies. More importantly, this simple method is expected to allow the large-scale production of other complex rare earth fluoride compounds with controllable morphologies and sizes, and exploration of the morphology and phase-dependent photoluminescence properties.