Microbial keratitis (MK) is the fourth leading cause of blindness globally, imposing a substantial burden on the healthcare system. This study aims to determine the cost composition of MK patients and explore factors influencing these expenses. We analyzed the demographics, clinical features, and costs of 602 MK patients treated at Beijing Tongren Hospital from June 2021 to October 2023. The analysis revealed the average total cost of treating MK was USD 1646.8, with a median of USD 550.3 (IQR: 333.3–1239.1). Patients with Acanthamoeba keratitis (AK) incurred the highest median total costs at USD 706.2 (IQR: 399.2–3370.2). Additionally, AK patients faced the highest costs for ophthalmic exams and laboratory tests (both p < 0.001), while patients with fungal keratitis (FK) and viral keratitis (VK) experienced higher medication costs. Costs varied significantly with the severity of MK, especially for outpatients at severity level 4, which was markedly higher than levels 1–3 (USD 1520.1 vs. USD 401.0, p < 0.001). Delayed presentation also resulted in increased costs (USD 385.2 vs. USD 600.3, p < 0.001). Our study highlights the financial burden associated with MK treatment and underscores the importance of timely and accurate diagnosis and intervention.