A suitable jump Markov system (JMS) filtering approach provides an efficient technique for tracking surface targets. In complex surface target tracking situations, due to the joint influences of lost measurements with an unknown probability and heavy-tailed measurement noise (HTMN), the estimation accuracy of conventional interacting multiple model (IMM) methods may be seriously degraded. Aiming to address the filtering issues in JMSs with HTMNs and random measurement losses, this paper presents an IMM filtering approach with the adaptive estimation of unknown measurement loss probability. In this study, we assumed that the measurement noises obey student’s t-distributions and then proposed Bernoulli random variables (BRVs) to characterize the random measurement loss. Notably, by converting the two likelihood functions from the weighted sum form to exponential multiplication, we established hierarchical Gaussian state space models to directly utilize the variational inference method. The system state vectors, unknown distribution parameters, BRVs, and unknown measurement loss probabilities were estimated simultaneously according to the variational Bayesian inference in the IMM framework. The results of maneuvering target tracking simulations verified that the presented filtering approach demonstrated superior estimation accuracy compared to existing IMM filters.