The shape of magnetic nanoparticles is of great importance in determining their contrast abilities for magnetic resonance imaging. Various magnetic nanoparticles have been developed to achieve high T1 or T2 relaxivities, but the mechanism on how morphology influences the water proton relaxation process is still unrevealed. Herein we synthesize manganese-doped iron oxide (MnIO) nanoparticles of the same volume with six different shapes and reveal the relationship between morphologies and T1/ T2 relaxation rates. The morphology of magnetic nanoparticles largely determines the effective radius and the gradient of stray field, which in turn affects the transverse relaxation rate. The longitudinal relaxivity has positive correlation with the surface-area-to-volume ratio and the occupancy rate of effective metal ions on exposed surfaces of magnetic nanoparticles. These findings together with the summary of r2/ r1 ratios could help to guide the screening for the optimal shapes of promising T1 or T2 contrast agents. Varying effective radii could be utilized to change negative contrast abilities. The surface-area-to-volume ratio and the amount of effective metal ions on exposed surface are instrumental for tuning positive contrast abilities. These principles could serve as guidelines for design and development of high-performance nanoparticle-based contrast agents.