For examining effects of atmosphere on system generated electromagnetic pulse (SGEMP), the external SGEMP are simulated by the 3D PIC code in pre-ionized plasma and by the PIC-MCC code in low pressure air respectively in the X-ray energy deposition region (50 km to 100 km). For three fluences of X-ray (4×10^-3 J/cm²、4×10^-2 J/cm²、0.4 J/cm²), the simulations are done in pre-ionized plasma corresponding to two different altitudes (70 km and 80-90 km) and low pressure air corresponding to 56 km altitude each other, and the results are compared with those in vacuum. The variation laws of external SGEMP in pre-ionized plasma and low pressure air are received : the effects have relation to fluence of X-ray, when the fluence of X-ray is low, the magnetic field increases and the electric field decreases in the plasma environment, while the variations of external SGEMP are not obvious in low pressure air; with the fluence of X-ray increasing, the space charge nonlinear effects become more and more obvious, the electric field and magnetic field are enhanced together in both pre-ionized plasma and low pressure air, and the enhancement effects are more significant in low pressure air.