The study on the influence of early age damage of concrete on its long-term strength development is of great importance. In this work, 102 concrete cubes with and without supplementary cementitious materials (SCMs) were prepared. The pre-loading with loading degrees of 20%, 50%, and 80% of the corresponding compressive strength at 3-, 7-, 14-, and 28 d age was applied to the concrete samples. Then, concrete samples were further cured to 270 d, and the compressive strength was tested by the uniaxial compression test. The acoustic emission signals during the compressive strength test were collected. It is found that the pozzolanic reaction healed the damage caused by the early age damage, and the compressive strength of concrete with the incorporation of SCMs at 270 d age after pre-loading was higher than that of ordinary concrete without SCMs. The peak frequency of the uniaxial compression acoustic emission of concrete can be divided into four frequency intervals to correspond to different damage mechanisms of concrete, namely: interval I (12 ± 5 kHz), interval II (38 kHz ± 5 kHz), interval III (171 kHz ± 5 kHz), interval IV (259 kHz ± 5 kHz).