In order to improve the surface quality of micro machined parts, micro milling experiments were designed to study the variations of surface roughness and sidewall residual burrs of micro grooves. First, from a theoretical point of view, the model of processed surface formation and micro machined surface roughness theory were introduced for the purpose of proposing changes to the sidewall for tool run-out. Then, typical parts were selected to process the micro straight grooves by the developed 3-axis linkage micro milling machine tool; the spindle speed, axial cutting depth, feed speed, tool run-out, and material organization structure on surface roughness were studied in depth. Finally, the milling surface roughness of the grooves was researched by adopting multiple factor orthogonal tests and analysis of extreme difference. The best surface roughness values for the three kinds of micro grooved bottoms made of aluminum alloy, steel, and titanium alloy are determined as 1.073-1.481 μm, 0.485-0.883 μm, and 0.235-0.267 μm, respectively. Without tool run out, the maximum height of the micro groove wall burr is found as 7.637 μm, and the maximum height of the micro-groove wall burr is found to be 21.79 μm when the tool has a radial composite runout of 0.3 μm. The experimental results show that the parameters are listed in the effective order given below: feed rate, spindle speed, and axial cutting depth. With the gradually increasing feed speed and axial cutting depth, the surface roughness Ra of the groove bottom gradually increased. However, increasing the spindle speed caused Ra to decrease and then increase. Under the same conditions, if the arc blades are without wear, the tool run-out on the micro straight groove sidewall surface quality has a greater impact. At the same time, different metal material properties are also potential factors affecting the surface quality of the micro channels.