In this paper, a new algorithm for fractional order system identification is set up. We study the structure of vector fitting and give a decomposition through the computational instance. In the vector fitting method, we use the complex least-square method to instead least-square method when calculating the residues and dealing with the errors based on vector fitting. And the rational fractional function has been extended from integer field to fractional domain. For validity, a comparison between the original and the present method is conducted.