Background: Bell's palsy is defined as idiopathic unilateral facial nerve palsy. Early Bell's palsy is characterized by emerging asymmetric motor conduction of the facial nerve and obvious imbalance of facial muscle movement, which can result in a substantial psychological impact on patients and trigger brain cortical functional reorganization. However, the differences between the brain functional alterations were driven by right or left facial nerve efferent dysfunction in patients with early Bell's palsy are not fully understood. The neuroimage study in patients with different-sided Bell's palsy in the early stage will help to understand the different mechanisms involved in functional integration driven by unilateral facial efferent nerve dysfunction and to provide the theoretical foundation for the choice of suitable treatment strategy. Methods: Sixty-seven patients and 37 age-and sex-matched healthy controls were recruited to undergo resting-state functional magnetic resonance imaging (R-fMRI). Regional brain activity was analyzed by comparing the fractional amplitude of low-frequency fluctuations (fALFF) between right palsy and healthy control, left palsy and healthy control, and right and left palsy groups. The altered brain regions were further selected as seeds in subsequent functional connectivity (FC) analysis, and the correlations between the Toronto Facial Grading System (TFGS) scores and the connectivity alterations were also analyzed. Results: The right and left Bell's palsy groups showed fALFF alterations compared with the healthy control group, and several brain regions with different fALFF values between the right and left palsy groups were identified. In the right palsy group, overall inter-regional FC increased in the right supramarginal gyrus (SMG), bilateral superior frontal gyrus (SFG), and left precentral gyrus (PreCG), compared with the left palsy group. Furthermore, the brain region pairs with higher FC in the right palsy group were left temporal pole of the superior temporal gyrus (TPOsup) and right SMG, left TPOsup and middle cingulate cortex (MCC), left TPOsup and left PreCG, right SMG and SFG, MCC and left PreCG, left and right SFG, and right SFG and left PreCG. In the right palsy group, the left TPOsup and PreCG showed a negative correlation with the TFGS score, while the right SFG and left PreCG showed a positive correlation with the TFGS scores. In the left palsy group, the left TPOsup and right SMG, and the right SMG and SFG region pairs showed a negative correlation with the TFGS score. Conclusions: The fALFF and FC analyses revealed the remodeling of different brain functional networks driven by right or left facial nerve efferent dysfunction in patients with early Bell's palsy. The reintegration mechanisms differed between patients with right and left Bell's palsy. Additionally, the severity of the disease showed different associations with altered FC.