This paper studies the trajectory tracking control of an autonomous underwater vehicle (AUV) based on a stochastic uncertain nonlinear system. We investigate the time-varying gain adaptive control method looking for possible approaches to alleviate the heavy computational burden. Under nonlinear growth, conditions satisfy polynomial growth conditions. These two problems are resolved the fast response time and good path tracking, respectively. Novel adaptive algorithms are developed exploiting the dynamic properties of the AUV motion. By appropriately turning the original controller design problems into parameters choosing problems and then solving them in a functional time-varying observer technical theorem. In order to deal with the station error of system converges to arbitrarily small domains with stochastic uncertain disturbance. A coordinate transformation is proposed for all system states to meet boundedness. We show that the convergence of the AUV trajectory errors can be guaranteed by the proposed contraction constraints in the stability analysis, closed-loop stability is proved, and the system is asymptotically probabilistic in the global scope. They are taking advantage of the guaranteed stability. Extensive simulation studies on the AUV model demonstrate the effectiveness and robustness of the proposed approach. A real-time time-varying gain constructive control strategy is further developed for the Hardware-in-the-loop simulation; the controller design results are imported into the AUV actuator model to verify the effectiveness of the controller design.