The objective of this research is to explore the relationships among various multidimensional factor groups and the density of fishery resources of ecosystems in offshore waters and to expand the application of deep machine learning algorithm in this field. Based on XGBoost and random forest algorithms, we first conducted regulatory importance ranking analysis on the time factor, space factor, acoustic technology factor, abiotic factor, and acoustic density of offshore fishery resources in the South China Sea. Based on these analyses, data slicing is carried out for multiple factors and acoustic density, and the relationship between multidimensional factor group and the density of marine living resources in the ecosystem of offshore waters is elaborately compared and analyzed. Importance ranking shows that the concentration of active silicate at 20 m depth, water depth, moon phase perfection, and the number of pulses per unit distance (Ping) are the first-order factors with a cumulative contribution rate of 50%. The comparative analysis shows that there are some complex relationships between the multidimensional factor group and the density of marine biological resources. Within a certain range, one factor strengthens the influence of another factor. When Si20 is in the range of 0–0.1, and the moon-phase perfection is in the range of 0.3–1, both Si20 and moon-phase perfection strengthened the positive influence of water depth on the density of fishery biological resources.