To address the issues of existing line boundary protection schemes, which are easily affected by transition resistance and lack effective parameter setting criteria, a flexible DC power grid line fault protection scheme based on the instantaneous frequency of transient voltage is proposed. First, an improved transient voltage gradient is used as the fault activation criterion. Then, the differences in transient voltage instantaneous frequency between the bus-side and the line-side of current-limiting reactors at both ends of the line under internal and external faults are analyzed. Singular value decomposition (SVD) is used to process the transient voltage signal. The instantaneous frequency (IF) is extracted from the first-level component obtained by the decomposition using the discrete energy separation algorithm (DESA), and a criterion for the internal/external fault is constructed based on the polarity of the integral difference. Finally, fault pole selection is realized according to the strength of the singularity of the second-layer component. Simulation results demonstrate that the proposed scheme can effectively identify fault zones, has strong resistance to transition resistance, and is robust against noise, current-limiting reactor size variations, line length changes, sampling frequency variations, and data synchronization errors.