Breast cancer is the most frequently diagnosed cancer in most countries. Early diagnosis of breast disease is necessary for its prognosis and treatment. Altered protein glycosylation has been shown to be expressed in precursor lesions of breast cancer, making them powerful early diagnostic biomarkers. The present study validated alterations of the N-glycan profiles of their salivary glycoproteins isolated by the Phaseolus vulgaris leucoagglutinin (PHA-E+L)-magnetic particle conjugates from 141 female subjects (66 healthy volunteers (HV), and 75 patients with breast disease including breast benign cyst (BB) or breast cancer in stage I/II (BC-I/II)) were analyzed and annotated by MALDI-TOF/TOF-MS. The results showed that there were 11, 20, 16, and 17 N-glycans recognized by PHA-E+L identified and annotated from the pooled salivary samples of HV, BB, BC-I, and BC-II, respectively. There were 3 N-glycans peaks (m/z 2459.8799, 2507.9139, and 2954.0547), 2 N-glycans peaks (m/z 1957.7265 and 2794.0427), and 2 N-glycans peaks (m/z 1866.6608 and 2240.8056) recognized by PHA-E+L that existed only in BB, BC-I, and BC-II, respectively. The present study compared the alternations of N-glycans from the salivary proteins isolated by PHA-E+L-magnetic particle conjugates among HV, BB, BC-I, and BC-II, which could provide information on N-glycans during the development of breast cancer in saliva to promote the study of its biomarkers.