Cilia are indispensable for the development and homeostasis of almost all organ systems, and compromised cilia structure and function lead to highly clinical and genetic heterogeneous diseases collected named as ciliopathy. Cilia biology and ciliopathy patho-mechanism remains largely underexplored. So far, cilia research field is lack of a tool that enable identifying cilia proteome in vivo under various physiological and pathological states. We generated cilia-targeted TurboID transgenic mice, and using these mice, we performed data-independent acquisition mass spectrometry (DIA-MS) to identify ciliary polypeptides from streptavidin captured proteomes in the brain and trachea tissues. These mice provide a valuable tool for dissecting ciliary proteomes under various physiological and diseased conditions, which will facilitate the discovering of underlying mechanisms of cilia biology and patho-mechanisms of ciliopathies in multiple organ systems.