In traditional underwater wireless sensor networks (UWSNs), it is difficult to establish reliable communication links as the acoustic wave experiences severe multipath effect, channel fading, and ambient noise. Recently, with the assistance of magnetic induction (MI) technique, cooperative multi-input-multi-output (MIMO) is utilized in UWSNs to enable the reliable long range underwater communication. Compared with the acoustic-based UWSNs, the UWSNs adopting MI-assisted acoustic cooperative MIMO are referred to as heterogeneous UWSNs, which are able to significantly improve the effective cover space and network throughput. Due to the complex channel characteristics and the heterogeneous architecture, the connectivity of underwater MI-assisted acoustic cooperative MIMO networks is much more complicated than that of acoustic-based UWSNs. In this paper, a mathematical model is proposed to analyze the connectivity of the networks, which considers the effects of channel characteristics, system parameters, and synchronization errors. The lower and upper bounds of the connectivity probability are also derived, which provide guidelines for the design and deployment of underwater MI-assisted acoustic cooperative MIMO networks. Monte Carlo simulations were performed, and the results validate the accuracy of the proposed model.