Water-jet guided laser (WJGL) machining is a novel processing technology using water beam fibers to guide the laser to machine the work-piece surface. This processing technology has the advantage of almost no micro-cracks, small heat-affected zone, pollution-free, less recast layer, high processing accuracy, parallel cuffing, etc. This work aims to investigate the effect of different WGLM parameters on the micro-morphology of materials and the mechanism between lasers and materials. The experiments for slotting and grooving 316L stainless steel thin samples were used by the WGLM system developed by our research group in this work. The 2D micro-topography after experiments were tested by the Zeiss Vert.A1 metalloscope, and the 3D micro-topography of samples after experiments were tested by the Leica DVM6 optical microscope with the large depth of field & Bruke Contour Elite I white-light interferometer. Experimental results show that a certain width deposition layer can be occurred in the machining region, and the width of deposition layers does not change with the parameter of the machining time and the number of machining times. From the 2D micro-topography of samples, it can be found that the ‘dr’ of slotting samples and the ‘wl’ of grooving samples also do not change with the machining parameters. From the 3D micro-topography of grooving samples, it can be found that the cross-section shape is inverted trapezoid.