This paper deals with a method for getting the Type III sums of squares on the basis of projections under the assumption of two-way fixed effects model. For unbalanced data in general total sum of squares is not equal to the sum of componentwise Type III sums of squares. There are some differencies between two quantities. The suggested method using projections can detect where the differences occur and how much they are different. The traditional ANOVA method could not explain clearly the differences. It also discusses how eigenvectors and eigenvalues of the projection matrices can be used to get the Type III sums of squares.