A shift control system and method of a hybrid vehicle are provided and controlled by dualizing a brake shift pattern based on whether an engine clutch release is possible when a hybrid vehicle brake is engaged. The system includes a hybrid controller that is configured to detect whether engine clutch release is possible, based on battery state information and input data from a operation. In addition, a shift controller is configured to execute a gear shift by a brake shift pattern based on whether the engine clutch release is possible.