A cross section of the rod is taken as object of investigation. The freedom of the section in free or constraint case is analyzed and the definition of virtual displacement of the section is given, which can be expressed by a variational operation. Assuming the variational and partial differential operations has commutativity, based on the hypothesis about surface constraint subjected to the rod, the freedom of the section on constraint surface is discussed and the equations satisfied by virtual displacements of the section are given. Combining D'Alembert principle and the principle of virtual work, D'Alembert-Lagrange principle is established. When constitutive equation of material of the rod is linear, the principle can be transformed to Euler-Lagrange form. From the principle, a dynamical equation in various forms such as Kirchhoff, Lagrange, Nielsen and Appell equation can be derived. For the case when a rod is subjected to a surface or a nonholonomic constraint, Lagrange equation with undetermined multipliers is obtained. Integral variational principle of dynamics of a super-thin elastic rod is also established, from which Hamilton principle formulation is obtained when the material of the rod is linear. Finally, canonical variables to describe the state of the section and Hamilton function are defined, and Hamilton canonical equation is derived. The analytical methods of dynamical modeling of a super-thin elastic rod have been constructed, which can serve as a theoretical framework of analytical dynamics of a super-thin elastic rod with two independent variables.