The phenomenon of bioclogging in porous media is widely present in nature and engineering and is closely related to fields such as the environment, energy, and basic medical care. In this work, we focus on the bioclogging process in porous media, and investigate the effects of flow rate and pore size on the behavior of biofilm clusters and the evolution of permeability by microfluidic chip-microscope-CMOS camera visualization experimental system. Flow-visualization experimental results show that flow rate and pore size control the surface morphology and ultimate clogging efficiency of biofilms by influencing shear rate and nutrient exchange rate. It is shown that bioclogging in the porous media presents two distinct clogging patterns, characterized by pattern I with preferential flow paths and pattern II without preferential paths. Pattern I occurs under conditions of smaller flow rate and larger pore size, the fluid mainly flows concentrated in in the preferential flow paths, the unevenness of this flow rate distribution will be exacerbated over time, affecting the stability of the clogging, the permeability decline shows obvious intermittent fluctuations. Pattern II occurs under conditions of higher flow rate and smaller pore size, the flow field distribution is relatively uniform with no obvious high-speed concentrated areas. In this pattern, the clogging effect is much more significant, with the permeability ratio being reduced by three orders of magnitudes at the end of experiments.