The partition function (PF) plays a key role in the calculation of quantum thermodynamic properties of a system that interacts with a heat bath. The imaginary-time hierarchical equations of motion (imHEOM) approach was developed to evaluate in a rigorous manner the PF of a system strongly coupled to a non-Markovian bath. In this paper, we present a numerically efficient scheme to evaluate the imHEOM utilizing the β-differentiated imHEOM (BD-imHEOM) that are obtained by differentiating the elements of the imHEOM with respect to the inverse temperature. This approach allows us to evaluate the system, system-bath interaction, and heat-bath parts of the PF efficiently. Moreover, we employ a polyharmonic decomposition method to construct a concise hierarchical structure with better convergence, thus reducing the cost of numerical integrations. We demonstrate the proposed approach by compute thermodynamic quantities of a spin-boson system and a 2 × 2 antiferromagnetic triangular spin lattice system with an Ohmic spectral distribution.