Introduction: The objective of this study was to investigate the prevalence, characteristics, and risk factors of acquired punctal stenosis (APS) in adult patients with allergic conjunctivitis (AC). Methods: This observational case series study included 210 adult AC patients at Zhongshan Ophthalmic Center. The demographic data were collected, and the ocular manifestations were assessed. Morphologies of AC patients’ lacrimal puncta were evaluated and graded using the modified grading system by slit-lamp microscopy. Results: There was 69.0% (145/210) of adult AC participants suffering from APS. Stenotic lacrimal puncta were present in 49.3% (414/840), with grade II<sub>a</sub> being the most common (54.6%). Abnormal upper lacrimal puncta were more frequent than lower ones (89.0% vs. 73.1%, p = 0.001). AC patients with APS were significantly older than those without APS (p < 0.001). The percentage of patients with tear meniscus height (TMH) >0.3 mm was 40% in the APS group, compared to 12.5% in the non-APS group (p < 0.001). The age (OR = 1.589, 95% CI: 1.109–2.276, p = 0.012) and TMH (OR = 3.449, 95% CI: 1.224–9.719, p = 0.019) were positively associated with the occurrence of APS. Conclusion: APS, especially the stenosis of upper lacrimal punctum, is frequently observed in the AC patients. Increased age and widened TMH are associated with the prevalence of APS in adult AC patients, suggesting a potential relationship between the long-term and recurrent course of AC and the development of APS.