We report on structural, compositional, and thermal characterization of self-assembled in-plane epitaxial Si1-xGex alloy nanowires grown by molecular beam epitaxy on Si (001) substrates. The thermal properties were studied by means of scanning thermal microscopy, while the microstructural characteristics, the spatial distribution of the elemental composition of the alloy nanowires and the sample surface were investigated by transmission electron microscopy and energy dispersive x-ray microanalysis. We provide new insights regarding the morphology of the in-plane nanostructures, their size-dependent gradient chemical composition, and the formation of a 5 nm thick wetting layer on the Si substrate surface. In addition, we directly probe heat transfer between a heated scanning probe sensor and Si1-xGex alloy nanowires of different morphological characteristics and we quantify their thermal resistance variations. We correlate the variations of the thermal signal to the dependence of the heat spreading with the cross-sectional geometry of the nanowires using finite element method simulations. With this method we determine the thermal conductivity of the nanowires with values in the range of 2-3 Wm-1K-1. These results provide valuable information in growth processes and show the great capability of the scanning thermal microscopy technique in ambient environment for nanoscale thermal studies, otherwise not possible using conventional tech-niques.