For the tracking control of n order MIMO affine systems with uncertainty, a nonlinear control method of command filtering backstepping with self-organizing approximation is proposed. A command filter with a saturation structure is used to eliminate the analytic computation of command derivatives, and compensated tracking errors are redefined to compensate the discrepancy between the command filtered signals and analytic computation of command derivatives. Command Filtered Backstepping is used to decouple the higher system and simplify the control structure. Self-organizing approximation is used to on-line approximate the uncertain and eliminate the effect of the uncertain to the tracking performance. The uncertain is approximated by a linear product between a set of basis functions and weighted functions on the local region. The weighted sum of compensated tracking errors is used as the prespecified tracking accuracy performance. When the prespecified tracking accuracy performance can not be achieved, a new local approximator is added to the control system according to the criterion based on Lyapunov theory to enhance the capacity of the approximator. Finally, an applications for a simple system is analyzed by simulations.