Aims: We examined differences in soil metabolites from the rice root rhizosphere of long-term rice-rice-fallow (RRF) and rice-rice-rape (RRR) rotations, and examined the effects of 1,2-benzenediol on nitrogen-use efficiency (NUE) and rice growth. Methods: The metabolite composition of rice rhizospheres was analyzed using the gas chromatography-mass spectrometry (GC-MS). A range of 0.2, 2.0 and 200 μmol L−1 concentrations of external 1,2-benzenediol were applied to examine their effects on rice growth, nitrate reductase (NR) and glutamine synthetase (GS) activities, and physiological nitrogen-use efficiency (PNUE). Results: The metabolite composition of rhizospheres differed significantly between RRR and RRF. Soil total N and 1,2-benzenediol concentrations during the early rice season were significantly lower under RRR than RRF. Rice growth and NUE significantly enhanced at 0.20 μmol 1,2-benzenediol L−1, but inhibited at 2.0 μmol L−1 or higher. Changes in root morphology and uptake associated with 1,2-benzenediol possibly had contributed to a higher NUE of the early season rice under RRR. The NR and GS activities in rice roots were significantly higher with 0.2 μmol L−1 1,2-benzenediol than without 1,2-benzenediol treatment. Conclusions: Crop rotation significantly affected rice rhizosphere metabolites. An optimal soil 1,2-benzenediol concentration under long-term RRR rotation may be associated with an enhanced NUE and root N uptake and assimilation, resulting in an increased rice growth and yield.