Based on the traditional linear regression model of guidance instrumental systematic error, the advantages and disadvantages of three parameter estimation methods were compared, namely Bayes estimate, principal component analysis and regularization method, and the practical limitations were presented. Combined with the specific initial error of sea-based missile, three estimation strategies named overall were designed, namely piecewise and iteration estimate strategy and giving detail estimate procedures, and the following separation steps were provided. Results show that the principal component analysis and regularization method are better than Bayes estimation, and the new proposed estimation strategies are better than the traditional one.