The invention discloses a detection method of diabetes B kidney deficiency salivary protein markers. The method comprises the following concrete steps of extracting sample protein; determining the extracted protein concentration by a Bradford method; performing proteolysis, iTRAQ marking, vacuum freeze centrifugation drying and reversed-phase chromatography separation under high pH conditions; performing protein analysis on ABI-5600; performing mass spectrometric data analysis; during database selection, if organisms are sequenced organisms, directly selecting the species databases; if the organisms are non-sequenced organisms, selecting main category proteome database most relevant to the tested sample; using an ABI-5600 type mass spectrograph to perform iTRAQ mass spectrograph analysis.The specific protein marker in the diabetes B kidney deficiency can be fast and reliably discovered by a proteomic technological scheme. A noninvasive, simple, convenient, fast and practical detectionand evaluation measure is built for the early diagnosis and treatment, postoperative recurrence, transfer and prognosis observation of the diabetes B kidney deficiency.