A low pressure EGR (Exhaust Gas Recirculation) system control apparatus of an internal combustion engine of a vehicle may include an atmosphere temperature detecting portion that detects atmosphere temperature of a driving region of the vehicle, an air conditioner switch that outputs ON/OFF signal of an air conditioner, a wiper switch outputting ON/OFF signal of a wiper, a control portion that uses the atmosphere temperature to determine a relative humidity and limits an operation of a low pressure EGR system such that condensate may be not formed therein, when the relative humidity may be higher than a predetermined humidity value.