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For urea Selective Catalytic Reduction (SCR) systems, adaptive control is of interest to provide a capability of maintaining high NOx conversion efficiency and low ammonia slip in the presence of uncertainties in the system. In this paper, the dynamics of the urea SCR system are represented by a control-oriented model which is based on a linear transfer function, with parameters dependent on engine operating conditions. The parameters are identified from input-output data generated by a high fidelity full chemistry model of the urea SCR system. The use of the full chemistry model facilitated the representation of the dynamics of stored ammonia (not a directly measurable parameter) as well as post SCR NOx and ammonia slip. A closed-loop Proportional-plus-Integral (PI) controller was first designed using the estimate of stored ammonia as a feedback signal.