Yearly increasing production of food waste is a great concern in Korea, and thus the use of processed-food waste as an alternative and/or additive resource to chemical fertilizer has been widely expanding. The food waste like a livestock manure includes abundant nutrients to promote crop growth and development, and the effect on crop growth and yield was confirmed from a variety of studies. In this study, we focused on investing primary metabolic perturbation affected by the application of food waste-livestock manure compost (FW-LMC) for rice production. The experiment employed six different levels of fertilization; no fertilization (NF), standard fertilization (SF, RDA guide), soil diagnosis fertilization (SDF) and SDF + FW-LMC (three different application levels, 1, 1.5 and 3.0 Mg ha -1 ). The rice (cv. Saechucheongbyeo) samples were taken at heading stage, carefully divided into the leaf blades and grains, and the targeted primary metabolites were profiled from the leaf blades and grains by GC-TOFMS. Glucose and fructose significantly declined in the leaf blade, and glucose, mannose and galactose tended to decrease in the grain, by contrast, sucrose was significantly greater. Pyroglutamic acid (increase in both organs), asparagine (increase in the leaf blade), β-alanine (increase in both organs) and tryptophan (increase in the leaf blade/decrease in the grain) were greatly perturbated. From the results, in terms of primary metabolism-based rice growth, it is summarized that the addition of FW-LMC in chemical fertilization (SF and SDF) could perturb primary metabolism, and affect not only vegetative growth of rice plants but also grain quality. Finally, the further study should be focused on understanding how the greater input of fertilization like the FW-LMC contributes grain qualities such as protein and amylose contents at the harvest stage.