We aimed to quantify the relative contributions of plant residue and organic manure to soil carbon sequestration. Using a 27-year-long inorganic fertilizer and manure amendment experiment in a maize (Zea mays L.) double-cropping system, we quantified changes in harvestable maize biomass and soil organic carbon stocks (0-20cm depth) between 1986-2012. By employing natural 13 C tracing techniques, we derived the proportional contributions of below-ground crop biomass return (maize-derived carbon) and external manure amendment (manure-derived carbon) to the total soil organic carbon stock. The average retention of maize-derived carbon plus manure-derived carbon during the early period of the trial (up to 11 years) was relatively high (10%) compared to the later period (22 to 27 years, 5.1-6.3%). About 11% of maize-derived carbon was converted to soil organic carbon, which was double the retention of manure-derived carbon (4.4-5.1%). This result emphasized that organic amendments were necessary to a win-win strategy for both SOC sequestration and maize production.