In the electron ion collider design, in order to achieve the peak luminosity 1034/cm 2/s with a reasonable lifetime, an efficient coherent electron cooling scheme was proposed to reduce the hadron beam emittance growth. Such a cooling scheme requires a good electron beam quality with a small energy spread. However, the shot noise in the electron beam through the accelerator might be amplified due to the microbunching instability and degrades the electron beam quality in the modulator section of the strong hadron cooling channel and correspondingly cooling rate. In this study, we report on self-consistent simulations of these effects using a real number of electrons to capture the details of shot noise and analysis of the shot noise growth through the accelerator.