The parallel connection of multiple coils can improve the power capacity, transmission efficiency and power density of the magnetics. However, there is a problem of unbalanced currents in the parallel branches because the self- and mutual inductances between multiple coil branches are not exactly the same, which leads to uneven losses in each coil branches and reduces the efficiency. Therefore, this paper proposes a segmented parallel compensation method to balance the coil currents, which can improve the system efficiency. However, the proposed method introduces high-frequency harmonic loop currents, which are suppressed by adding differential mode inductors. Firstly, the circuit is modeled and the current balancing condition is analyzed to get the segmented parallel compensation parameter design method. Then, the coil harmonics loop currents are analyzed before and after adding the differential mode inductors. Finally, a 2 kW prototype was built. The system efficiency was improved by up to 1.05% under heavy load compared to traditional method.