The invention discloses a method and system for separate relief of pressure of a locomotive braking cylinder. The method comprises the steps that a separate relief instruction generated by an instruction generator is received, and a second braking instruction generated by a small brake is controlled to relieve the pressure of a first pre-controlled air cylinder (5) according to a comparison result of a first preset pressure value P1 and a second preset pressure value P2, so that the pressure of the locomotive braking cylinder is P2; a separate relief electric pneumatic valve (10) is controlled to be powered on, so that a separate relief exhaust valve (8) is switched on, and the pressure of a second pre-controlled air cylinder (13) is output through the separate relief exhaust valve (8) which is switched on. By means of the method, the pressure of the locomotive braking cylinder controlled by the small brake is maintained, and the pressure of the locomotive braking cylinder controlled by a big brake is relieved; hence, abrasion to braking components at the time of locomotive braking is reduced, the service life of a braking system is prolonged, and then the use cost of the braking system is lowered.