In the present work, an attempt was made to engineer a mesoporous silica coated magnetic nanoparticles (MNF@mSiO2) for twin mode contrast in magnetic resonance imaging (MRI) with reduced toxicity. Superparamagnetic manganese ferrite nanoparticles were synthesized with variable mesoporous silica shell thickness to control the water molecules interacting with metal oxide core. 178 nm was the optimum hydrodynamic diameter of mesoporous ferrite core-shell nanoparticles that showed maximum longitudinal relaxation time (T1) and transverse relaxation time (T2) in MRI due to the storage of water molecules in mesoporous silica coating. Besides the major role of mesoporous silica in controlling relaxivity, mesoporous silica shell also reduces the toxicity and enhances the bioavailability of superparamagnetic manganese ferrite nanoparticles. The in vitro toxicity assessment using HepG2 liver carcinoma cells shows that the mesoporous silica coating over ferrite nanoparticles could exert less toxicity compared to the uncoated particle.