In the present paper, YbVO4 microcrystals with diverse morphologies, sizes and dimensions have been synthesized via a mild and controllable hydrothermal process using trisodium citrate (Na3Cit) as an organic additive. The phases, morphologies, sizes, and photoluminescent properties of the as-prepared products were well characterized by means of X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT–IR), scanning electron microscopy (SEM), transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM), and up-conversion (UC) luminescence, respectively. The results indicate that the morphology and size of the YbVO4 samples can be tuned in a controlled manner by altering the amount of Na3Cit, pH value of the initial solution, and the reaction time. The possible formation mechanism for products with diverse architectures has been presented in detail. The UC luminescence properties as well as the emission mechanisms of YbVO4:Ln3+ (Ln3+ = Er3+, Tm3+, Ho3+) microcrystals were systematically investigated, which show green (Er3+, 4S3/2, 2H11/2 → 4I15/2), blue (Tm3+, 1G4 → 3H6) and red (Ho3+, 5F5 → 5I8) luminescence under 980 nm NIR excitation. Furthermore, the experimental results also reveal that the optical properties of the YbVO4:Er3+/Ho3+ phosphors with different morphologies are strongly dependent on their morphologies and sizes.