The present study tries to identify proteins implicated in bradycardia rabbits in hearts after ShenSongYangXin (SSYX, a traditional Chinese medicine) treatment. Eighteen adult rabbits were randomly assigned to three groups: sham, model, and SSYX treatment groups. Heart rate was recorded in rabbits and proteins were isolated from ventricular muscle. We used isobaric tags for elative and absolute quantitation (iTRAQ) coupled with two-dimensional liquid chromatography-tandem mass spectrometry to identify altered proteins after SSYX treatment. The heart rate decreased after six weeks due to the injury of the sinoatrial node in the model group. This effect was partially reversed by 4-week SSYX treatment. A total of a2988 proteins were quantified by performing the iTRAQ-based experiments. Of these, 86 proteins were differentially expressed according to our criteria (42 upregulated and 44 downregulated). The identification of key proteins implicated in the treatment of bradycardia could serve as a foundation to better understand and further explore the molecular mechanism of SSYX treatment.