Bipolar junction transistors (BJTs) are often used in spacecraft due to their excellent working characteristics. However, the complex space radiation environment induces primary knock-on atoms (PKAs) in BJTs through collisions, resulting in hard-to-recover displacement damage and affecting the performance of electronic components. In this paper, the properties of PKAs induced by typical space heavy ions (C, N, O, Fe) in BJTs are investigated using Monte Carlo simulations. The simulated results show that the energy spectrum of ion-induced PKAs is primarily concentrated in the low-energy range (17 eV–100 eV) and displays similar features across all tested ions. The PKAs induced by the collision of energetic ions have large forward scattering angles, mainly around 88°. Moreover, the distribution of PKAs within a transistor as a function of depth displays a peak characteristic, and the peak position is linearly proportional to the incident energy at a certain energy range. These simulation outcomes serve as crucial theoretical support for long-term semiconductor material defect evolution and ground testing of semiconductor devices.