In this paper, a new defective phononic crystal (PC) microbeam model in a thermal environment is developed with the application of modified couple stress theory (MCST). By using Hamilton’s principle, the wave equation and complete boundary conditions of a heated Bernoulli–Euler microbeam are obtained. The band structures of the perfect and defective heated PC microbeams are solved by employing the transfer matrix method and supercell technology. The accuracy of the new model is validated using the finite element model, and the parametric analysis is conducted to examine the influences of size and temperature effects, as well as defect segment length, on the band structures of current microbeams. The results indicate that the size effect induces microstructure hardening, while the increase in temperature has a softening impact, decreasing the band gap frequencies. The inclusion of defect cells leads to the localization of elastic waves. These findings have significant implications for the design of microdevices, including applications in micro-energy harvesters, energy absorbers, and micro-electro-mechanical systems (MEMS).