This paper proposes a new method for determining the correction factor of a newly developed waveguide primary power measurement system (i.e., microcalorimeter), based on the electromagnetic field theory analysis for waveguide thermal isolation section (TIS) in foil short measurement mode. The new method determines the contribution of the power dissipated within the TIS into the correction factor, in term of the physical dimensions of the TIS. Performance comparison and analysis show that the newly proposed method can significantly reduce the measurement uncertainty when evaluating the correction factor of waveguide microcalorimeters.