X-ray fluorescence computed tomography (XFCT) is a molecular imaging technique with great potential applications in biomedical imaging, in which used is the primary X-ray to excite element probes with high atomic number inside samples or tissues for functional imaging. However, owing to the limitation of molecular sensitivity and spatial resolution, the XFCT has not been widely used in the molecular imaging. A large number of Compton scattering photons are produced as the broadband primary X-ray passes through the samples or tissues, forming a strong noise background in the collected XRF signal, which is a major cause of limited molecular sensitivity. Therefore, eliminating the Compton scattering noise is very important for improving molecular sensitivity. In this paper, we summarize the main physical processes involved in the imaging process of XFCT, including the angle distribution and polarization state of the fluorescence and Compton scattering photons, fluorescence yield and deexcitation time of K-shell vacancy. The above physical processes are the main limitations of the imaging quality of XFCT. Through the derivation and analysis of physical processes, we explore the possibility of using these physical effects to reduce the Compton scattering noise and draw some conclusions below. 1) The deexcitation time of K-shell vacancy of the element with high atomic number is very short, consequently the scattered light and fluorescence cannot be distinguished between each other under the time resolution condition of the existing detector. 2) The angular distribution of the K-shell fluorescence emission is isotropic, and the differential cross section of Compton scattering reaches a minimum value near the polarization direction of the incident light of which the minimum decreases as the linear polarization degree of the incident light increases. Therefore, the polarized light source is beneficial to reducing the Compton scattering noise. 3) The linear degree of polarization of K-shell fluorescence is zero, while the Compton scattering photons possess a certain linear degree of polarization in some scattering directions, so the difference between polarization states may be helpful in reducing the Compton scattering noise.