Degradation of scaffolds is an important problem in tissue regeneration management. This paper reports a comparative study on degradation of the printed 3D poly (lactic-co-glycolic acid) scaffold under three conditions, namely, micro-channel, incubator static, and incubator shaking in the phosphate buffer saline (PBS) solution. In the case of the micro-channel condition, the solution was circulated. The following attributes of the scaffold and the solution were measured, including the mass or weight loss, water uptake, morphological and structural changes, and porosity change of the scaffold and the pH value of the PBS solution. In addition, shear stress in the scaffold under the micro-channel condition at the initial time was calculated with Computational Fluid Dynamics (CFD) to see how the shear stress factor may affect the morphological change of the scaffold. The results showed that the aforementioned attributes in the condition of the micro-channel were significantly different from the other two conditions. The mechanisms that account for the results were proposed. The reasons behind the results were explored. The main contributions of the study were (1) new observations of the degradation behavior of the scaffold under the micro-channel condition compared with the conditions of incubator static and incubator shaking along with underlying reasons, (2) new understanding of the role of the shear stress in the scaffold under the condition of the micro-channel to the morphological change of the scaffold, and (3) new understanding of interactions among the attributes pertinent to scaffold degradation, such as weight loss, water uptake, pH value, porosity change, and morphological change. This study sheds important light on the scaffold degradation to be controlled more precisely.