Ocean Acoustic Tomography (OAT) is an important marine remote sensing technique used for inverting large-scale ocean environmental parameters, but traditional methods face challenges in computational complexity and environmental interference. This paper proposes a causal analysis-driven AI FOR SCIENCE method for high-precision and rapid inversion of oceanic hydrological parameters in complex underwater environments. Based on the open-source VTUAD (Vessel Type Underwater Acoustic Data) dataset, the method first utilizes a fine-tuned Paraformer (a fast and accurate parallel transformer) model for precise classification of sound source targets. Then, using structural causal models (SCM) and potential outcome frameworks, causal embedding vectors with physical significance are constructed. Finally, a cross-modal Transformer network is employed to fuse acoustic features, sound source priors, and environmental variables, enabling inversion of temperature and salinity in the Georgia Strait of Canada. Experimental results show that the method achieves accuracies of 97.77% and 95.52% for temperature and salinity inversion tasks, respectively, significantly outperforming traditional methods. Additionally, with GPU acceleration, the inference speed is improved by over sixfold, aimed at enabling real-time Ocean Acoustic Tomography (OAT) on edge computing platforms as smart hardware, thereby validating the method’s practicality. By incorporating causal inference and cross-modal data fusion, this study not only enhances inversion accuracy and model interpretability but also provides new insights for real-time applications of OAT.