In 2024–2025, the global maritime industry faced a paradox: simultaneously with a steady decline in the number of cases of total loss of vessels, a noticeable increase in operational incidents was recorded, driven by failures of mechanical equipment, the share of which in the overall accident structure reached 60%. Against this background, bunkering operations, previously perceived as a technologically refined and largely routine procedure, under conditions of stricter environmental regulation and a widespread transition to very low sulfur fuels (VLSFO, LSMGO), were transformed into a key element of the risk profile of shipping. The purpose of the study is to develop a comprehensive mathematical and organizational model for ensuring the safety of bunkering operations, integrating statistical analysis of accident rates, the technical characteristics of highly loaded shipboard equipment (including MFP-540 type pumps and plate heat exchangers), and regulatory prescriptions. The methodological basis is built on a meta-analysis of statistical datasets of ITOPF, EMSA, and leading protection and indemnity clubs (Gard, NorthStandard) for the period 2020–2025. As the key analytical toolkit, the failure modes and effects analysis (FMEA) method was applied, implemented using fuzzy logic apparatus (Fuzzy Logic), as well as mathematical modeling of viscosity–temperature characteristics of marine fuels in accordance with the ASTM D341 standard. The results of the analysis conducted during the study showed that 64.5% of registered incidents have a root cause associated with the human factor; however, a hidden systemic driver of accident occurrence is the technical incompatibility of aging ship power and auxiliary systems with the operating modes of modern equipment. It was established that MFP-540 type pumps at an operating pressure of 1300 psi, as well as plate heat exchangers, are characterized by critical vulnerability to the temperature gradient during the transition from one fuel type to another (HFO/MGO), which creates prerequisites for the development of thermal shock and cavitation damage. The proposed integrated model Safe Ops demonstrated the ability to reduce the risk of the specified damage by optimizing the modes and algorithms for conducting bunkering operations, which is expressed in a reduction of the integral risk priority number (RPN) by 35%. The implementation of the proposed control algorithms, harmonized with the requirements of international instruments regarding the closed method of bunkering and the regulated delineation of responsibility between the master and the chief engineer, constitutes a necessary condition for maintaining the required level of shipping safety under contemporary operational and regulatory conditions