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In this paper, microscopic characteristics of preformed gels (PGs) and secondary cross-linked gels (SCG) with the same concentration were analyzed by atomic force microscopy (AFM). Experimental results indicate that the microstructure of secondary cross-linked gels is a thick 3-D network, in which micro-holes and irregular macro-holes are embedded. The maximum width of the irregular macro-holes is 200 nm. In the SCG, two different chemical bonds were formed, which leads to the structural inhomogeneity and the asymmetry of the crosslinking density. The structural inhomogeneity of SCG results in the formation of irregular macro-holes. The excessive cross-linking density is the primary reason for dehydration of SCG and the presence of irregular macro-holes in SCG can facilitate dehydration.