Heavy ion irradiation effects on charge trapping memory (CTM) capacitors with TiN/Al2O3/HfO2/Al2O3/HfO2/SiO2/p-Si structure have been investigated. The ion-induced interface charges and oxide trap charges were calculated and analyzed by capacitance–voltage (C–V) characteristics. The C–V curves shift towards the negative direction after swift heavy ion irradiation, due to the net positive charges accumulating in the trapping layer. The memory window decreases with the increase of ion fluence at high voltage, which results from heavy ion-induced structural damage in the blocking layer. The mechanism of heavy ion irradiation effects on CTM capacitors is discussed in detail with energy band diagrams. The results may help to better understand the physical mechanism of heavy ion-induced degradation of CTM capacitors.