With the development of global maritime trade, ship emissions pose an increasing threat to the global atmospheric environment, especially in international navigation waters and important port areas, where their impact on coastal air quality and ecosystems is becoming increasingly significant. This study proposes a high-throughput gridding algorithm (H-Grid) based on spatial hashing to rapidly generate ship emission inventories, which overcomes the inefficiency of traditional methods caused by complex index building and maintenance. The H-Grid algorithm achieves a constant processing time per data point and possesses inherent parallelism. Based on the H-Grid algorithm, taking the Yellow Sea area between China and Republic of Korea as a case study, the emissions of atmospheric pollutants from ships in 2024 were calculated, and their spatiotemporal distribution characteristics were analyzed. In our empirical study, the algorithm’s computational efficiency for processing millions of AIS records was improved by over 10 times compared to traditional geometric calculations, and by more than 4 times when compared to mainstream database spatial queries. Our findings provide an efficient tool for large-scale maritime emission analysis, strongly supporting the green development of global shipping.