A thermomechanical equivalent continuum (TMEC) theory is developed for the deformation of atomistic particle systems at arbitrary size scales and under fully dynamic conditions. This theory allows continuum interpretation of molecular dynamics (MD) model results and derivation of thermomechanical continuum constitutive properties from MD results under conditions of general macroscopically transient thermomechanical deformations, which are not analysed by statistical mechanics. When specialized to the more specific conditions of non-deforming systems in macroscopic equilibrium, this theory yields certain results that are identical to, or consistent with, the results of statistical mechanics. Coupled thermomechanical continuum equations and constitutive behaviour are derived using MD concepts in a time-resolved manner. This theory is a further advancement from the purely mechanical equivalent continuum (EC) theory developed recently. Within the meaning of classical mechanics, the TMEC theory establishes the ultimate atomic origin of coupled thermomechanical deformation phenomena at the continuum level. The analysis is based on the decomposition of atomic particle velocity into a structural deformation part and a thermal oscillation part. On one hand, balance of momentum at the structural level yields fields of stress, body force, traction, mass density and deformation as they appear to a macroscopic observer. On the other hand, balance of momentum for the thermal motions relative to the macroscopically measured structure yields the fields of heat flux and temperature. These quantities are cast in a manner as to conform to the continuum phenomenological equation for heat conduction and generation, yielding scale-sensitive characterizations of specific heat, thermal conductivity and thermal relaxation time. The structural deformation and the thermal conduction processes are coupled because the equations for structural deformation and for heat conduction are two different forms of the same balance of momentum equation at the fully time-resolved atomic level. This coupling occurs through an inertial force term in each equation induced by the other process. For the structural deformation equation, the inertial force term induced by thermal oscillations of atoms gives rise to the phenomenological dependence of deformation on temperature. For the heat equation, the inertial force term induced by structural deformation takes the phenomenological form of a heat source.