Incredible accomplishments have been achieved in agricultural production in China, but many demanding challenges for ensuring food security and environmental sustainability remain. Field experiments were conducted from 2011-2013 at three different sites, including Honghu, Shayang, and Jingzhou in China, to determine the effects of fertilization on enhancing crop productivity and indigenous nutrient-supplying capacity (INuS) in a rice (Oryza sativa L.)-rapeseed (Brassica napus L.) rotation. Four mineral fertilizer treatments (NPK, NP, NK and PK) were applied in a randomized complete block design with three replicates. Crop yields were increased by 19-41% (rice) and 61-76% (rapeseed) during the two years of rice-rapeseed rotation under NPK fertilization compared to PK fertilization across the study sites. Yield responses to fertilization were ranked NPK > NP > NK > PK, illustrating that N deficiency was the most limiting condition in a rice-rapeseed rotation, followed by P and K deficiencies. The highest and lowest N, P and K accumulations were observed under NPK and PK fertilization, respectively. The INuS of the soil decreased to a significant extent and affected rice-rapeseed rotation productivity at each site under NP, NK, and PK fertilization when compared to NPK. Based on the study results, a balanced nutrient application using NPK fertilization is a key management strategy for enhancing rice-rapeseed productivity and environmental safety.