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In this paper,we have combined penalty method and adaptive finite element method to simulate incompressible Navier-Stokes equations.We first give two types of error estimators,then present three kinds of numerical experiments.The first numerical example is to verify the convergence results of [Int.J.Inf.Syst.Sci.2(2006) 131-143].The other two numerical experiments are to affirm the reliability and efficiency of error estimator.It was found that our adaptive penalty finite element method can save large lots of work.