A waste heat recovery system has a Rankine cycle in which boilers, an expander, a condenser, and a circulation pump are installed on a circulation path in which working fluid is circulated, and the boilers are connected in series with and in parallel to the circulation path. The waste heat recovery system includes: a first and a second direction control valves installed at a top and at a bottom of the boilers to shift flow directions of the working fluid to the boilers; and a controlling unit to receive information of a vehicle and information of the waste heat recovery system to control the first and second direction control valves.