As a fault occurs on lines of a two-terminal low-frequency transmission system, fault currents will be suppressed when frequency converters adopt negative sequence current suppression strategy. Under such a circumstance, currents on both sides of the line show weak feed and traversal characteristics, leading to poor sensitivity or even failure to operate of the traditional phase-based line differential protection. To solve the above problem, the two-terminal low-frequency transmission system based on modular multilevel matrix converter (M3C) topology is constructed. And the fault electrical characteristics and phasor differential protection adaptability of single-phase grounding and two-phase short-circuit faults of low-frequency lines are analyzed. Then, a fault control strategy is proposed to highlight fault characteristics by suppressing the positive sequence current output of the power control station, thereby improving the braking characteristics and sensitivity of differential protection. Finally, a real-time digital simulator (RTDS) model is built based on a low-frequency transmission project, and the proposed control strategy is simulated and verified against typical faults. The results show that the proposed fault control strategy can effectively solve the problem of insufficient sensitivity of phasor differential protection for low-frequency line fault, being of well value in engineering application.