Obstructive sleep apnea syndrome is generally associated with multiple cardiovascular disorders, such as myocardial hypertrophy. Autophagy is strictly modulated to maintain cardiac homeostasis. Post-injury autophagy is closely associated with pathological cardiac hypertrophy. BCL2 interacting protein 3 (BNIP3) and BNIP3-like protein (BNIP3L) can cause cell death and are important for hypoxia-elicited autophagy. Here, we evaluated whether BNIP3 could mitigate functional remodeling and cardiac hypertrophy through regulation of autophagy. Male WT rats or rats with BNIP3 knockout were subjected to chronic intermittent hypoxia (CIH) for 8 h/day over 5 weeks. Echocardiography and morphology were employed to assess the cardioprotective effects. Autophagy was assessed via transmission electron microscopy and detection of LC3, p62, and Beclin-1. Terminal deoxynucleotidyl transferase dUTP nick end labeling and the Bax/Bcl2 ratio were used to monitor apoptosis. Biochemical evaluations were performed to assess oxidative stress. Additionally, BNIP3-knockdown H9c2 cells that were subjected to CIH were used to examine autophagy and apoptosis to confirm the findings of the animal study. The CIH group showed elevated heart weight/body weight and left ventricle weight/body weight proportions, along with left ventricular remodeling. CIH-exposed rats exhibited dramatically higher fractional shortening and ejection fractions than the controls. In addition, the levels of autophagy markers Beclin-1 and LC3-II/I were increased, whereas the level of p62 was reduced by CIH treatment. The oxidative marker levels and the apoptosis index in the CIH group were markedly increased. Knockout of BNIP3 significantly aggravated the impairment in cardiac function, apoptosis, oxidative stress, and hypertrophy of CIH rats, while significantly reducing autophagy. The autophagy-associated PI3K/Akt/mTOR pathway was also deactivated by BNIP3 knockout. At the cellular level, CIH treatment significantly upregulated autophagy and apoptosis; however, BNIP3 silencing reduced autophagy and promoted apoptosis. CIH treatment-mediated upregulation of BNIP3 expression plays a crucial role in autophagy by targeting the PI3K/Akt/mTOR pathway, alleviating cardiac hypertrophy.