Formation damage caused by well drilling, completion, oil testing, oil recovery, and stimulation seriously affects oil and gas production, the evaluation of which plays an important role in the process of oilfield development. Thus, it is necessary to study formation damage mechanism from micro scale. In this study, two sets of displacement experiments were conducted using two sandstone samples and two chemical reagents. Each set was divided into three processes: first formation water injection, reverse chemical reagents injection and second formation water injection. According to the results of displacement experiments, the permeability changes of two sandstone samples were analyzed and the formation damage rates of different experimental processes were calculated respectively. In addition, we analyzed the formation damage of the two samples from the macroscopic aspect according to the changes of inlet pressure curves. We compared the pore structure changes of sandstone samples at different experiment processes by computed tomography (CT) images, and found the particle migration phenomenon. Based on the core sensitive regions observed by CT images, the pore network models of the sensitive regions were extracted to quantitatively characterize the change of pore structure parameters (pore radius, throat radius, coordination number and tortuosity). Finally, we designed a two-dimensional microscopic seepage channel model according to the real core structure. The flow rule of solid particles in fluid was simulated by finite element method, and the reason of reservoir clogging was analyzed. Through this study, we found that the injection of chemical reagents increased the inlet pressure and led to the decrease of core permeabilities. There was a negative correlation between the export rate of particle migration and matrix deformation degree.