In order to solve the problem including huge calculated amount and confirming the weights un- reasonably which exist in multi- target orthogonal test method, multi-target orthogonal test design was optimized by matrix analysis. Three-layer structure model and the layer structure matrix of orthogonal test were established firstly, thenweight matrix of test index can beworked out by matrix of each layer multiples cation and the weighs of the factors and levels having influences on the tests' results can be calculated. Fi- nally the optimal plan and the important order of the factors' influences on the tests' index values can be determined according to the weights. The results show that the problem of selecting the optimal plan in multi-target orthogonal test design can be solved very well.