Effects of different kinds of fertilizer and application methods on tomato yields and inorganic nutrient contents were investigated. The contribution of nitrogen usage to tomato production for each fertilizer application was also estimated by the stable isotope ratio of nitrogen. LSR (low sulfate slow-release fertilizer, LSR plot), daily application of liquid OK-F-1 fertilizer (OK-F-1 plot) and PEL (manure pellet fertilizer, PEL plot) yielded most among the eight different treatments. Fruit quality as measured by nitrogen content (related to amino acid content) was higher in the OK-F-1 treatment. In the conventional fertilization of mixing fertilizer in soil, roots absorbed soil nitrogen which affected the δ¹⁵N values of fruits, while in the daily application of liquid fertilizer (fertigation) there was little observed influence of soil nitrogen on the δ¹⁵N values of the upper parts of tomato. These results suggested that fertigation is an effective fertilization method which preserved soil nitrogen.