Cobalt chromium (CoCr) alloy tubes have been widely used in manufacturing of vascular stents, due to their excellent bio-mechanical properties, especially their high strength. In recent years, fiber lasers have been used in the micro-machining of vascular stents, given their better cutting quality than neodymium-doped yttrium aluminum garnet (Nd:YAG) lasers. A comparison study of CoCr fiber laser cutting with oxygen and argon is presented, and the differences, such as surface topography, chemical composition, and kerfs geometry, between the oxygen cuts and argon cuts are studied. Three types of topographies are obtained for the oxygen cuts, and the underlying reason for the different topographies are discussed. The influences of key parameters including power, repetition rate, pulse width, and cutting speed on the cutting quality are analyzed. The present research can also provide an optimization guideline for the micro-profiling of CoCr vascular stents.