Objective This paper investigates the effects of the endothelial glycocalyx layer (EGL) and hypertension on macromolecular transport in the arterial walls to provide a theoretical method to understand the occurence of atherosclerosis. Methods We estabilish a five-layer porous media model to simulate macromolecular transport. The artery is assumed to be an axisymmetric circular tube and plasma is Newtonian fluid. Theoretical analysis is used to obtain filtration velocity and macromolecular concentration under steady-state flow condition. Results The effect of EGL’s thickness on filtration velocity can be neglected. With the increase of EGL’s thickness, the resistance of macromolecular transport becomes more obvious. The existence of EGL decreases the effect of the hypertension on macromolecular transport. Conclusions EGL offers rather high resistance to macromolecular permeation. Even under hypertension condition, the increase of macromolecular concentration within the intima is not obvious. In the presence of EGL, the excessive macromolecule penetration into the arterial walls caused by hypertension can be prevented effectively.