Sperm-specific CatSper1 and CatSper2 proteins are critical to sperm hyperactivated motility and male fertility. Although architecturally resembling voltage-gated ion channels, neither CatSper1 nor CatSper2 alone forms functional ion channels in heterologous expression systems, which may be related to the absence of yet unidentified accessory subunits. Here we isolated CatSper1 and CatSper2 associated protein(s) from human sperm and analyzed their identities by Multidimensional Protein Identification Technology (MudPIT) approach. We identified the T-type voltage-gated calcium channel Cav3.3 as binding to both CatSper1 and CatSper2. The specificity of their interactions was verified by co-immunoprecipitation in transfected mammalian cells. Electrophysiological studies revealed that the co-expression of CatSper1 or CatSper2 specifically inhibited the amplitude of Cav3.3-evoked T-type calcium current without altering other biophysical properties of Cav3.3. Immunostaining studies revealed co-localization of CatSper1 and Cav3.3 on the principal piece of human sperm tail. Further, Fluorescence Resonance Energy Transfer (FRET) analysis revealed close proximity and physical association of these two proteins on the sperm tail. These studies demonstrate that CatSper1 and CatSper2 can associate with and modulate the function of Cav3.3 channel, which might be important in the regulation of sperm function.