A shift control system of an automatic transmission and a method thereof include controlling the off-going and on-coming clutches according to hydraulic pressures of the off-going and on-coming clutches calculated based on a flare amount when a flare occurs, controlling the on-coming clutch according to hydraulic pressure of the on-coming clutch calculated based on a shifting time interval when the flare does not occur and the shifting time interval is smaller than or equal to a predetermined time interval, and controlling the off-going and on-coming clutches according to hydraulic pressures of the off-going and on-coming clutches calculated based on an excess rate of change of a turbine speed when the shifting time interval is larger than a predetermined time interval.