Because of special structure and dynamic behavior, the dynamic equations of metamorphic mechanism are variable during the process of configuration change. In order to combine dynamics analysis and structure design of metamorphic mechanisms intimately, a new method of forming dynamic model of metamorphic mechanisms is proposed based on fully Cartesian coordinate’s method and the relation between origin mechanism and sub-configuration. A new concept named origin constraint equation is introduced which can be converted into constraint equations of each sub-configuration easily by adding corresponding constraint equations of configuration change. Constraint equations commonly used in configuration change and dynamic equations of each configuration are given in the form of natural coordinates. Finally, a four-bar spherical metamorphic mechanism is used as an example to validate this dynamic modeling method.