In view of validation of simulation model, ordinary gray relational analysis (GRA) usually stresses similarity but ignores nearness between the simulations and flight-tests time series, while the nearness is part of model error. To reduce the risk in application of GRA, a new matrix gray relational analysis was proposed, which is in view of the similarity and the nearness between the simulations and flight-test time series. The new model can also solve the relational analysis problem with many characteristics of behavior and the operational steps were listed in detail. It is proved that the improved model satisfies the four gray relational axioms. Finally, a case study was given to show the reasonability and validity of the improved model.