Thermoplastics composites for structural applications are under growing development from the aerospace (carbon fibers with PEI, PPS or PEEK matrices mainly) to the automotive industry (glass and carbon fibers with PP, PA). The plastic deformation they can provide and the assembly facilities through welding techniques are well appreciated. Among the available welding technics, laser offers the possibility to assemble materials in a precise and localized manner and can be easily automated. However, due to the presence of continuous fibers at a high fiber volume fraction, propagation of the laser energy through the composite that present local variation of fiber volume fraction is not as straight forward as in a homogeneous material. Modelling of the laser welding of a thermoplastic/continuous glass fiber is considered here. The study takes into account the microstructure of the composite in order to evaluate changes in local energy absorption and diffusion directly linked with the thickness. Modelling of the welding process is developed from the representation of the moving laser beam. The beam propagation through the composite thickness is considered thanks to the ray tracing method. The proposed method is able to optimise the welding process in function of the microstructure and the material properties of the welded parts.