With the increasing exploitation and use of marine resources, the limitations of acoustic, optical, and radio frequency technologies for underwater communications have become increasingly apparent. Magnetic induction (MI) is a new communication technology that enables wireless data transmission via magnetic field coupling between transmitting and receiving coils. MI offers advantages such as channel stability, small antenna size, and no multi-path loss. Multi-input–multi-output (MIMO) is a multi-antenna technology that significantly increases system capacity and spectrum utilization without increasing bandwidth. The whale optimization algorithm (WOA) is a well-known bio-inspired algorithm that mimics the hunting behavior of whales to optimize swarm intelligence. This paper proposes a model for an underwater MIMO communication system based on magnetic induction. We then construct a signal detection algorithm for MI-MIMO systems using the advanced whale optimization algorithm (AWOA) and conduct simulation experiments to compare the performance and complexity of three standard signal detection algorithms: zero-forcing (ZF), minimum mean square error (MMSE), and maximum likelihood (ML). The experimental results show that AWOA achieves suboptimal results, as its bit error rate (BER) is close to that of the ML algorithm. Furthermore, the complexity of AWOA is comparable to that of the MMSE strategy. This work supports the development of a high-performance MI-based underwater communication system.