Glycosylation is one of the most common and important post-translational modifications of proteins. Identification of large-scale N-linked glycoprotein is a very important aspect in glycoproteomics research. The N-glycopeptide enrichment is a key step in high-throughput identification of N-glycosylation site. Lectin enrichment and hydrazide chemistry are the two widely used N-glycopeptides enrichment methods. Each method can only enrich certain types of glycopeptides. It has been reported that the two methods are highly complementary, but few studies compared overlaps of glycosties from the two methods. In this paper, using HepG2 cells, we systematically compared the performance of hydrazide chemistry and lectins enrichment methods. The results showed that although the hydrazide method with glycopeptides enrichment efficiency of 76.7%, far higher than the 54.6% lectin enrichment method, 825 glycoprotein and 1 879 N-glycosylation sites identified with the lectin method was significantly more than 522 glycoprotein and 1 014 glycosylation sites enriched by the hydrazide method. Moreover, the two methods did not show significant complementary, together, only 853 glycoproteins and 1 959 N-glycosylation sites were identified. The overlapping results of identified N-glycosylation sites and N-glycoproteins from the two methods show that lectins enrichment method was better than hydrazide chemistry method.