A braking control system and a braking control method for an environmental-friendly vehicle may forcibly discharge a part of the current charge amount of a battery when it is determined that the current charge amount of the battery reaches a maximum charge amount state by regenerative braking to exclude a regenerative braking prohibition condition according to the maximum charge amount state of the battery. The braking of the vehicle is thereby always performed by a sum of the regenerative braking amount and the hydraulic braking amount to reduce a braking load concentrated on a disk of a hydraulic braking brake.