The implementation of the IMO 2020 regulation (MARPOL Annex VI), limiting marine fuel sulphur content to 0.5% m/m, has introduced new operational challenges to the Pertamina International Shipping fleet operating Wärtsilä 7RT-flex 58T and MAN Mitsui engines equipped with common rail systems. Indonesian LSFO supplied from local bunker sources exhibits very low kinematic viscosity (3–21 mm²/s at 50 °C) far below the global VLSFO average of approximately 80–105 mm²/s and has been associated with a series of incidents including compression-area oversizing, piston ring breakage, and cylinder liner cracking. This paper addresses these challenges through a systematic analysis of the cylinder lubrication strategy, comprising: (1) comprehensive characterization of three representative Indonesian LSFO samples from Cilacap, a Jakarta blend, and a Singapore baseline (2) evaluation of combustion chamber condition under various cylinder oil configurations and (3) analysis and evaluation of cylinder oil Base Number (BN) and feed rate. The methodology integrates fuel characterization (ASTM D445, D4052, HFRR ISO 12156-1, SARA D2007), engine testing over 27 screening combinations (3 fuels × 3 BN × 3 feed rates, 25 hours per condition) followed by validation of the 9 best combinations (100 hours per condition), and deposit characterization via XRD, SEM-EDS, and Vickers microhardness. The results confirm the predictions of VPS (2020) and Schildhauer (2019) that pairing BN 40 cylinder oil with low-sulphur LSFO causes abrasive CaCO₃ deposit accumulation (62% w/w by Rietveld refinement), triggering wear rates 4–5 times above normal. The best performing combination is identified at BN 25 with a feed rate of 0.7 g/kWh for low-sulphur Indonesian LSFO (Samples A and B), yielding iron content of 145–170 ppm, stable reserve BN of 28–35%, and wear rates of 0.016–0.022 mm/1000 h all well within acceptable thresholds while the baseline Sample C retains its optimum at BN 40 with 0.9 g/kWh, consistent with international practice. A viscosity- and sulphur-based decision tool is developed as a practical output and is projected to save USD 245 thousand per vessel-year (26.5%) compared with current baseline operation, supporting the safe, reliable, and economical implementation of Indonesian LSFO under the IMO 2020 regime.