The transition between nanoscale and microscale thermal transport regime at room temperature in silicon wires with constant and periodically modulated cross-section is theoretically investigated. Extrapolating the calculated thermal conductivity from the nano- to micrometer range, we find the characteristic dimensions of the wires where a crossover between nanoscale and microscale thermal transport occurs. This crossover is observed in both generic (smooth) and cross-section-modulated wires. In case of smooth silicon wires, we reveal a strong dependence of the crossing point position on the boundary roughness. For silicon wires with weak boundary roughness, the crossover occurs at cross-sections ∼60 nm × 300 nm, while for very rough boundaries it occurs at cross-sections ∼150 nm × 750 nm. In case of the periodically modulated wires, the crossover between nano- and microscale regimes occurs at typical cross-sections ∼120 nm × 120 nm of the narrow segment, and it is almost independent of boundary roughness. A strong distinction from the case of smooth wires is attributed (i) to the different trends at the nanometer scale, wherefrom the extrapolation was performed, and (ii) to the different phonon-boundary scattering due to the specific geometry. For modulated silicon wires, the influence of modulation thickness, modulation length, and cross-sectional area on the phonon thermal conductivity at the room temperature is analyzed. A possibility of thermal transport engineering in cross-section-modulated wires by resizing them is revealed in both nano- and microscale regimes. The presented results pave the way towards a better understanding of thermal transport reduction in Si nanowires with engineered diameter modulations and shed light on the crossover between nano- and microscale regimes of thermal transport.