The purpose of this paper is to investigate the clinical diagnostic value of the C13 urea breath test in the detection of Helicobacter pylori infection. The methodology of this study was to select 100 patients with epigastric discomfort who visited our hospital from January 2022 to July 2023. All patients underwent rapid urease test (RUT) and C13-urea breath test. Histological examination was used as the diagnostic gold standard to compare the diagnostic accuracy of the two methods for various diseases in patients, including the diagnostic positive rate. The diagnostic performance of the two methods (sensitivity, specificity, accuracy, negative predictive value, positive predictive value) was assessed. Results Of the 100 patients with epigastric discomfort is that 90 were diagnosed by pathologic examination. The C13-urea breath test had a higher diagnostic positive rate for duodenitis and peptic ulcers compared to RUT (P<0.05). There was no significant difference in the diagnostic positive rate between the two methods for gastric polyps, chronic gastritis, and gastric cancer (P>0.05). The C13-urea breath test had higher sensitivity, specificity, accuracy, positive predictive value, and negative predictive value compared to RUT. The specificity and accuracy of the two methods were significantly different (P<0.05), while the sensitivity, negative predictive value, and positive predictive value were not significantly different (P>0.05). This paper concludes that both the C13-urea breath test and the RUT are effective diagnostic methods for detecting H. pylori infection, but the C13-urea breath test has a higher diagnostic positivity rate and overall diagnostic performance. It provides a strong basis for clinical diagnosis and treatment, and has high clinical value. Therefore, it is worth promoting.