This article presents a new method of estimation of thermo-physical parameters using the hybrid Monte Carlo (HMC) algorithm that synergistically combines the advantages of a Markov Chain Monte Carlo method and molecular dynamics. The advantages of this technique over the conventional Markov Chain Monte Carlo are elucidated by considering multi-parameter estimation in heat transfer. Four situations were analyzed. The first two involve a two and a three parameters estimation in a lumped capacitance model, third involves estimation in a distributed system and the fourth involves estimation in a fin system. The goal is to establish the potency and usefulness of the HMC method for a wide class of engineering problems.