Oil pollution influences marine biology, ecology, and regional sustainable development capacity, but model uncertainties limit the ability of the numerical model to accurately predict the transport and fate of the underwater oil spill. Based on a three-dimensional underwater oil spill model validated by satellite images of the oil slick at the sea surface, the Penglai 19-3 oil spill accident in the Bohai Sea was simulated; in addition, several sensitivity experiments were set up to investigate the influence of model uncertainties in the background wind, current, start time of the oil spill, and spill site on the transport of underwater spilled oil in the Penglai 19-3 oil spill accident. The experimental results indicate that the uncertainty in the background wind has a certain impact on the simulated centroid position at the sea surface, and little effect on the simulated underwater results, while the uncertainty in the background current has a significant influence on the transport of the underwater spilled oil both at the sea surface and underwater. An uncertainty of 24 h in the start time of the oil spill can cause more than 1 time larger than the benchmark case displacement of the oil spill centroid point and sweeping area at the sea surface, as the periodic tidal current is the main constituent of the ocean current in the Bohai Sea. The uncertainty in the spill site has a large influence on the final position of the oil spill centroid point, but the oil spill trajectories do not intersect with each other within 48 h, which makes it possible to identify the oil spill platform from the actual observations. The influence of uncertainties in the important model inputs and key model parameters on the transport of underwater spilled oil in the Penglai 19-3 oil spill accident is evaluated for the first time, which is of substantial significance for improving the prediction accuracy of the transport and fate of underwater oil spills.