The invention discloses a control method and system for a bypass of a secondary reheating coal-fired power unit. The control method comprises the step that when the high-pressure bypass meets a preset judgment condition, a high-pressure bypass starting mode is adopted for operation. According to the mode, whether the initial pressure of an outlet of a boiler is higher than the extremely-hot starting pressure of a unit or not is judged, a pressure regulating valve of the high-pressure bypass is opened to a first high-pressure bypass opening degree according to the judgment result, the opening degree is maintained till the main steam pressure reaches a first expected value, and the main steam pressure is maintained at the first expected value without being changed; when the pressure regulating valve of the high-pressure bypass is opened to a second high-pressure bypass opening degree, the opening degree is kept unchanged, and the main steam pressure is increased to a first turning pressure; and after the unit turns and is connected to a grid, the pressure regulating valve of the high-pressure bypass is closed, the main steam pressure changes according to a unit sliding pressure curve, opening-preventing pressure for the pressure regulating valve of the high-pressure bypass is superposed on the sliding pressure curve, and when the actual main steam pressure cannot keep the pressure regulating valve of the high-pressure bypass closed, an overflow operating mode is started. By adoption of the scheme, whole-flow automatic control over the bypass of the secondary reheating coal-fired power unit can be achieved.