Background: Morphological differences in the temporomandibular joint (TMJ) are crucial for the treatment of patients with cleft lip and palate (CLP). This study aims to evaluate and compare the TMJ parameters in patients with unilateral and bilateral CLP across growing and non-growing age groups using cone-beam computed tomography (CBCT). Methods: CBCT records from 57 patients (23 males and 34 females) aged 6–50 years with a diagnosed unilateral or bilateral CLP were analyzed. Patients were categorized into four groups: growing unilateral (UGCLP), growing bilateral (BGCLP), non-growing unilateral (UNGCLP), and non-growing bilateral (BNGCLP). Measurements of TMJ parameters, including the mandibular fossa, articular eminence inclination, joint spaces, and roof thickness of the glenoid fossa, were conducted using CBCT images. Results: Significant differences were observed in the anterior joint space (AJS) and the roof of the glenoid fossa (RGF) between growing and non-growing unilateral cleft patients. Additionally, significant discrepancies were found in the articular eminence angle when comparing the cleft and non-cleft sides within the unilateral growing group. No significant differences were observed in TMJ parameters between the right and left sides among bilateral cleft patients. Conclusions: The study highlights distinct TMJ morphological differences between growing and non-growing patients with CLP, emphasizing the importance of age-specific considerations in the treatment planning and growth monitoring of these patients.