In order to properly handle the problem of fault isolation in the hybrid High Voltage DC (HVDC) transmission system, a fault isolation method based on the coordination of a Fault Current Limiter (FCL) and a DC Circuit Breaker (DCB) is proposed. The structure and modeling of FCL and DCB are expounded, and the timing coordination scheme of the two devices is designed. Considering the transient stages of the FCL action and the DCB operating, the fault equivalent circuit of the hybrid DC transmission system is built, and the mathematical equations of the peak current, dissipated energy and fault clearance time are theoretically derived. Using a PSCAD/EMTDC platform, a 320 kV class hybrid HVDC transmission test system is built. Different current limiting resistances, main breaker delays and fault severities are simulated, and the transient behaviors of the system are compared. The simulation results verify the positive effects of the proposed method on inhibiting the short-circuit current, speeding up fault isolation, and reducing the dissipated energy in the DCB. The effectiveness and adaptability of the proposed method in the hybrid HVDC transmission system are confirmed. This work is supported by Science and Technology Project of the Headquarter of State Grid Corporation of China “Study on overvoltage and insulation coordination of hybrid HVDC system with LCC-VSC” (No. SGTYHT/16-JS-198).