With the increasing requirement of Reynolds number simulation in wind tunnel tests, the cryogenic wind tunnel is considered as a feasible method to realize high Reynolds number. Characteristic model-based adaptive controller design method is introduced to flow field control problem of the cryogenic wind tunnel. A class of nonlinear multi-input multi-output (MIMO) system is given for theoretical research that is related to flow field control of the cryogenic wind tunnel. The characteristic model in the form of second-order time-varying difference equations is provided to represent the system. A characteristic model-based adaptive controller is also designed correspondingly. The stability analysis of the closed loop system composed of the characteristic model or the exact discrete-time model and the proposed controller is investigated respectively. Numerical simulation is presented to illustrate the effectiveness of this control method. The modeling and control problem based on characteristic model method for a class of MIMO system are studied and first applied to the cryogenic wind tunnel control field.