Optimizing and fully understanding the dynamic culture conditions in tissue engineering could accelerate exploration of this new technique into a promising therapy in the medical field. Scaffolds used in tissue engineering usually are highly porous with various pore architecture depending on techniques that manufacture them. Perfusing culture fluid through a scaffold in a bioreactor has proven efficient in enhancing the exchange of nutrients and gas within cell-scaffold constructs. Upon perfusion, flowing fluid in pores inevitably produces shear stress on the wall of the pores, which will in turn induce cellular response for the cells possessing mechanotransducers. Thus, establishing a relationship between perfusion rate, fluid shear stress and pore architecture in a 3-dimensional cell culture environment is a challenging task faced by tissue engineers because the same inlet flow rate could induce local variation of flow rate within the pores. Until recently, there is no proper non-destructive monitoring technique available that is capable of measuring flow rate in opaque thick objects. In this study, chitosan scaffolds with altered pore architectures were manufactured by freeze-drying or porogen leaching out or alkaline gelation techniques. Doppler optical coherence tomography (DOCT) has been used to differentiate the flow rate pattern within scaffolds which have either elongating pore structure or homogeneous round pore structure. The structural and flow images have been obtained for the scaffolds. It is found that pore interconnectivity is critically important in obtaining a steady flow under a given inlet flow rate. In addition, different internal pore structures affect local flow rate pattern.