Bowtie filters are used to modulate an incoming x-ray beam as a function of the angle of the x-ray to balance the photon flux on a detector array. Because of their key roles in radiation dose reduction and multi-energy imaging, bowtie filters have attracted a major attention in modern X-ray computed tomography (CT). However, few researches are concerned on the effects of the structure and materials for the bowtie filter in the Cone Beam CT (CBCT). In this study, the influence of bowtie filters’ structure and materials on X-ray photons distribution are analyzed using Monte Carlo (MC) simulations by MCNP5 code. In the current model, the phantom was radiated by virtual X-ray source (its’ energy spectrum calculated by SpekCalc program) filtered using bowtie, then all photons were collected through array photoncounting detectors. In the process above, two bowtie filters’ parameters which include center thickness (B), edge thickness (controlled by A), changed respectively. Two kinds of situation are simulated: 1) A=0.036, B=1, 2, 3, 4, 5, 6mm and the material is aluminum; 2) A=0.016, 0.036, 0.056, 0.076, 0.096, B=2mm and the material is aluminum. All the X-ray photons' distribution are measured through MCNP. The results show that reduction in center thickness and edge thickness can reduce the number of background photons in CBCT. Our preliminary research shows that structure parameters of bowtie filter can influence X-ray photons, furthermore, radiation dose distribution, which provide some evidences in design of bowtie filter for reducing radiation dose in CBCT.