Carbon (C) and nitrogen (N) inputs to farmland via fertilizer application are potential sources of C and N that influence soil acidification and water eutrophication. A pilot study was conducted to compare the effects of compound fertilizer and rapeseed cake organic fertilizer on C and N preservation in the soils and runoff of a tea plantation as well as the C and N isotopic fractionation in soils over the three annual cycles of fertilization and tea-leaf harvest. Overall, rapeseed cake organic fertilization effectively increased the pH, total organic matter, NH-N and NO-N in soils by 2.19-4.29%, 8.04-21.14%, 53.65-100.32% and 5.74-54.08%, respectively, but decreased NH-N inputs in runoff by 10.36-25.12% and NO-N inputs in runoff by 8.94-24.10% relative to the same rate of pure N in compound fertilizer. Before fertilization in February, the average δC and δN were -25.15‰ and 1.88‰, while after a full year of fertilization and tea-leaf harvesting in October, the average soil δC and δN contents were -23.83‰ and -0.33‰ after compound fertilization and -26.22‰ and 1.64‰ after rapeseed cake organic fertilization, respectively, indicating the evident effects of fertilization on the isotopic fractionation in soil. In addition, the fractionation extent was positively associated with the fertilization rates under both fertilizers. However, the two fertilization types had different effects on the C and N isotope fractionations, with rapeseed cake organic fertilization contributing more to δC (21.07-81.80%) but less to δN (18.20-78.93%) and compound fertilization presenting the opposite results (1.88-46.18% and 53.82-98.12%, respectively). This study demonstrates that rapeseed cake organic fertilization can better preserve soil C and N pools while reducing their runoff in tea plantations, which may greatly hinder the regional soil acidification and water eutrophication trends.