A porous structure is the key factor to successful chromatography separation. Agarose gel as one of the most popular porous media has been extensively used in chromatography separation. As the cooling process in the agarose gelation procedure can directly influence the pore structure, ten kinds of 4% agarosemedia with different cooling rates from 0.132 to 16.7 degrees C/min were synthesized, and the pore structure was determined accurately by using low-field NMR spectroscopy. The curves of pore structure and cooling rate can be divided into two stages with the boundary of 6 degrees C/min. In stage I, the pore structure met a power equation with the decrease of the cooling rate, and in stage II, the process reached a plateau. Confirmatory experiments proved that, by adjusting the cooling rate, a precise control of the pore structure of agarose media can be realized, furthermore, cooling rate optimization was an effective way to control the pore size of agarose media and can further tailor the pore structure for more effective separation of different proteins.