Background: Sinonasal polyposis (SNP) is a common inflammatory condition characterized by the growth of polyps within the nasal cavity and paranasal sinuses, often influenced by sinonasal anatomical variations. These variations, such as deviated nasal septum (DNS) and concha bullosa, can affect sinus drainage and contribute to disease severity. A thorough understanding of these anatomical differences is crucial for optimizing surgical and medical management. Method: A descriptive cross-sectional study was conducted at a tertiary care center over one year to evaluate the prevalence of sinonasal anatomical variations in patients with SNP. Patients aged 17 years or older, unresponsive to 3–4 weeks of standard medical treatment, were included. Data collection involved clinical examinations, patient interviews, and computed tomography (CT) imaging to identify anatomical variations. Statistical analysis was performed using SPSS version 24.0, with descriptive statistics to determine prevalence and inferential statistics to assess relationships between variations and disease severity. Results: Out of 100 patients with SNP, 86.11% exhibited at least one sinonasal anatomical variation. Agger nasi cells (79%) and DNS (72.5%) were the most prevalent, followed by concha bullosa (24%). Patients with multiple anatomical variations (60%) had significantly higher Lund Mackay scores (16.76 ± 4.6) compared to those with a single variation (4.67 ± 1.73), indicating greater disease severity (P-value = 0.000). Conclusion: Sinonasal anatomical variations are highly prevalent in patients with SNP and significantly influence disease severity. Preoperative CT imaging is essential for visualizing these variations, guiding surgical planning, and minimizing complications during functional endoscopic sinus surgery (FESS). Understanding both common and rare variants enhances patient outcomes through tailored interventions.