Background Malocclusion is a common dental condition that affects both function and aesthetics, influencing oral health-related quality of life (OHRQoL). Factors such as salivary composition, dental arch form, tongue posture, and muscle tone play a role in its development. Understanding the biological and functional aspects of malocclusion can help in early diagnosis and management to improve overall well-being.This study aimed to assess the relationship between oral biology and malocclusion and its impact on OHRQoL among individuals at Khyber Medical University. Methods A cross-sectional study was conducted from January 2023 to January 2024, involving 89 participants recruited from outpatient dental clinics. Clinical examinations were performed to assess malocclusion severity based on Angle’s classification, overjet, and overbite measurements. Salivary characteristics, including pH and flow rate, were analyzed using laboratory methods. The ‘Oral Health Impact Profile-14 (OHIP-14) questionnaire was used to evaluate the impact of malocclusion on quality of life’. Data were analyzed using SPSS version 25, with chi-square tests applied to determine associations, considering p-values below 0.05 as statistically significant. Results The study found that moderate to severe malocclusion significantly affected OHRQoL, with a notable impact on self-perception, social interactions, and functional limitations. ‘OHIP-14 scores were significantly associated with malocclusion’ severity (p = 0.026), indicating a strong link between poor dental alignment and reduced quality of life. While variations in salivary pH and flow rate were observed, their direct relationship with malocclusion was inconclusive. Aesthetic concerns were common, with 39.3% of participants dissatisfied with their dental appearance. Functional limitations, including difficulty in chewing and speaking, were reported by 42.7% of participants. Conclusion The study highlights the impact of malocclusion on OHRQoL, emphasizing the importance of early orthodontic intervention to improve both function and psychological well-being. While the role of salivary characteristics in malocclusion requires further research, the findings reinforce the need for timely dental assessment and treatment. Future studies with larger sample sizes can provide deeper insights into the biological and functional aspects of malocclusion.