In this paper, we extend the Cappell-Miller analytic torsion to manifolds with boundary under the absolute and relative boundary conditions and using the techniques of Brüning-Ma and Su-Zhang, we get the anomaly formula of it for odd dimensional manifolds. Then by the methods of Brüning-Ma, Cappell-Miller and Su-Zhang, we get the CheegerMüller theorem for the Cappell-Miller analytic torsion on odd dimensional manifolds with boundary up to a sign. As a consequence of the main theorem, we get the gluing formula for the Cappell-Miller analytic torsion which generalizes a theorem of Huang.