N-glycosylation, as a common post-translational modification with enormous structures, plays key roles in protein folding, cellular recognition and signaling pathways. State-of-the-art mass spectrometry-based N-glycoproteomics has enabled deep N-glycoproteome characterization of various human organs. However, a comprehensive N-glycoproteome landscape of human organs remains lacking. Here we present a systematic human N-glycoproteome atlas spanning 18 organs/tissues with identification of 31,003 intact N-glycopeptides, corresponding to 14,043 N-glycan monosaccharide compositions on 5,539 N-glycosites of 3,681 N-glycoproteins. Tissue-specific glycosylation patterns, novel glycoforms and crosstalk between sialylation and fucosylation are observed. This atlas, complemented by a unified multi-software analysis framework, provides insights into organ-specific glycobiology and establishes a fundamental reference for understanding physiological glycosylation characteristics of human tissues.