Microscopic density matrix analysis on the linewidth enhancement factor (LEF) of both mid-infrared (mid-IR) and Terahertz (THz) quantum cascade lasers (QCLs) is reported, taking into account of the many body Coulomb interactions, coherence of resonant-tunneling transport and non-parabolicity. A non-zero LEF at the gain peak is obtained due to these combined microscopic effects. The results show that, for mid-IR QCLs, the many body Coulomb interaction and non-parabolicity contribute greatly to the non-zero LEF. In contrast, for THz QCLs, the many body Coulomb interactions and the resonant-tunneling effects greatly influence the LEF resulting in a non-zero value at the gain peak. This microscopic model not only partially explains the non-zero LEF of QCLs at the gain peak, which observed in the experiments for a while but cannot be explicitly explained, but also can be employed to improve the active region designs so as to reduce the LEF by optimizing the corresponding parameters.