At present, the line protection of a flexible DC grid mostly depends on boundary components. This is not suitable for a "mesh structure" flexible DC grid with no obvious boundary between lines. Given the problem of line protection in long-distance transmission, an inverse time overcurrent protection configuration scheme independent of boundary components is proposed. First, by analyzing the transient characteristics of fault current, the requirements of protection configuration in different fault locations are determined. Then, based on protection requirements and using the wave head characteristics of fault current, the resistance compensation coefficient is constructed to ensure the resistance to transition resistance of the scheme. The action equation of inverse time overcurrent protection suitable for the fault characteristics of a flexible DC grid is established, and the calculation and setting principle of time delay are determined. Finally, the effectiveness and applicability of the scheme are verified based on the PSCAD/EMTDC simulation platform. The results show that the proposed scheme can accurately and reliably identify faults and has strong resistance to transition resistance.