A subject-specific model of instantaneous cost of transport (ICOT) is introduced from the joint-space formulation of metabolic energy expenditure using the laws of thermodynamics and the principles of multibody system dynamics. Work and heat are formulated in generalized coordinates as functions of joint kinematic and dynamic variables. Generalized heat rates mapped from muscle energetics are estimated from experimental walking metabolic data for the whole body, including upper-body and bilateral data synchronization. Identified subject-specific energetic parameters-mass, height, (estimated) maximum oxygen uptake, and (estimated) maximum joint torques-are incorporated into the heat rate, as opposed to the traditional in vitro and subject-invariant muscle parameters. The total model metabolic energy expenditure values are within 5.7 ± 4.6% error of the measured values with strong (R2 > 0.90) inter- and intra-subject correlations. The model reliably predicts the characteristic convexity and magnitudes (0.326-0.348) of the experimental total COT (0.311-0.358) across different subjects and speeds. The ICOT as a function of time provides insights into gait energetic causes and effects (e.g., normalized comparison and sensitivity with respect to walking speed) and phase-specific COT, which are unavailable from conventional metabolic measurements or muscle models. Using the joint-space variables from commonly measured or simulated data, the models enable real-time and phase-specific evaluations of transient or non-periodic general tasks that use a range of (aerobic) energy pathway similar to that of steady-state walking.