In the liquid metal (LM) blanket design for magnetic confinement fusion reactors, manifolds including main and branch ducts are commonly used to direct fluids to various locations of the blanket to cool its components. The primary objective of this structural configuration is to achieve flow balancing within each branch duct. However, magnetohydrodynamic effects will cause uneven flow distribution, consequently, uncontrollable overheating phenomena in certain blanket segments may be caused by this flow distribution. To assess its impact, the influences of external magnetic fields, inlet velocities and coupling wall thicknesses on the flow partitioning in conductive manifolds are investigated in this study. The results indicate that the flow distribution among the branch ducts becomes less uniform as the external magnetic field strength increases, while varying the inlet velocity has minimal impact. In addition, increasing the coupling wall thickness leads to more even flow distribution when the rectangular branch ducts are perpendicular with the magnetic field direction. Based on above physical understanding, three controlling methods for the flow partitioning in conductive manifolds are proposed to achieve flow balancing in each branch duct and then validated through numerical simulations. The results indicate that flow balancing can be achieved by adjusting the coupling wall thickness when the rectangular branch ducts are aligned with the magnetic field direction, however, it is challenging when they are perpendicular. Furthermore, the flow balancing can be realized by a symmetrical design of the manifold with circular branch pipes and it is independent of external magnetic fields and inlet velocities. These findings will enhance the physical understanding of flow distribution patterns in conductive manifolds under strong magnetic fields, which is important for the flow control and design of manifolds in LM blankets.