Objective: To compare the bacterial distribution of patients with chronic dacryocystitis from southern China and northwest China and to elucidate the geographical differences in the bacterial spectrum. Methods: This retrospective cross-sectional study included patients diagnosed with chronic dacryocystitis at the ophthalmology departments of tertiary hospitals in southern and northwest China between March 2022 and April 2024. Endoscopic dacryocystorhinostomy was performed on all patients to collect lacrimal sac secretions. The specimens were cultured for bacteria and fungi, and the positive rates and composition ratios of bacterial culture were compared between the two groups. Results: The positive rates of bacterial cultures from lacrimal sac secretions were 26.0% in southern China and 50.7% in northwest China (P < 0.001). The proportions of Gram-positive cocci and Gram-negative bacilli were 45.9% and 37.6%, respectively, in southern China, compared to 71.4% and 19.0%, respectively, in northwest China (P = 0.007 and P = 0.003, respectively). Coagulase-negative staphylococci were the most frequently detected bacteria in both regions. However, the proportion of Streptococcus species was significantly higher in northwest China compared to southern China (P = 0.004). Conclusions: The positive rate of lacrimal sac secretion cultures was lower in southern China compared to northwest China. The bacterial spectrum of chronic dacryocystitis in both regions was predominantly composed of Gram-positive bacteria. However, the proportion of Gram-negative bacteria was higher in southern China, while the detection rate of Streptococcus species was significantly higher in northwest China. These differences may be attributed to variations in climate, geographical features, and lifestyle habits.