This investigation intends to analyze the influence of nanoparticles morphology on the magnetic flux dependent thermo-physical properties and magnetohydrodynamic free convection heat transfer performance of water-based magnesium ferrite ferrofluid under various volume fractions. The thermo-physical parameters of the ferrofluid suspended with cube shaped particles are examined at 25 °C using KD2 pro thermal analyzer, Ostwald viscometer and specific gravity bottle under magnetic flux. The free convection heat transfer is obtained using heat pipes assisted cubical enclosure. Without the influence of magnetic flux, the thermal conductivity of the ferrofluid was improved by a maximum of 12.75% at a volume fraction of 0.15%. At the same time, the maximum viscosity and density were raised by 32.92% and 6.11% at a volume fraction of 0.20% in comparison with water. Under the influence of 350 Gauss, thermal conductivity, and viscosity of ferrofluid enhanced by 21.81% and 37.41% while the density decreased by 4.91%. It was revealed that the addition of cube-shaped magnesium ferrite particles in ferrofluid improved the thermo-physical properties. The optimum concentration for maximum heat transfer is reduced to 0.025% with the use of cube shaped particles compared to other types of nanoparticles reported in previous studies.