Organic matter found in early Martian sediment1-4 may help in defining early Martian environmental conditions and provide the key to understanding Mars’ prebiotic chemistry and habitability. However, the origin of this organic matter remains uncertain. Anomalous 13C depletion was recently discovered in this organic matter5, and has the potential to elucidate their origins, though plausible mechanism to cause the strong 13C depletion is unknown. Here, we present experimental and theoretical studies which demonstrated that solar ultraviolet photolysis of CO2 yields strongly 13C-depleted CO. In a reducing atmosphere, isotopically anomalous CO is converted into organic molecules that are deposited into sediments. Therefore, atmospheric synthesis of organics from CO is a plausible mechanism to explain the presence of organics in early Martian sediments and its strong 13C depletion. Furthermore, this mechanism could explain 13C enrichment of early Martian CO2 without the aid of long-term carbon escape into space. A mass balance model calculation using the estimated isotopic fractionation factor indicated approximately 20% conversion of volcanic CO2 into organics via CO, which satisfied the available data for carbon isotopes. Consequently, our results suggest that considerable amounts of organic matter may have been synthesized in a reducing early Martian atmosphere and stored within sediment.