The effects of exogenous inorganic [i.e., nitrate (NO3-)/ammonium (NH4+)] and organic [i.e., glutamate (Glu)/argine (Arg)] N alone and in combination on the accumulation of proline (Pro) in rice plant under trivalent chromium [Cr(III)] stress were studied through the mass balance matrix model (MBMM). ‘NH4+’ application showed the largest contribution to the Pro content in rice shoots under different concentrations of Cr(III), followed by ‘NO3-’, ‘Arg’, and ‘Glu’ application respectively. While, ‘Arg’ application displayed the largest contribution to the Pro content in roots under Cr(III) stress, followed by ‘NH4+’, ‘Glu’, and ‘NO3-’ application. Among the combination cases of N sources used, the application of ‘NH4++Arg’ showed the greatest contribution to the Pro content in both roots and shoots of Cr(III)-treated rice seedlings, while the application of ‘NO3-+Glu’ showed the least contribution to the Pro content in rice seedlings under Cr(III) stress. Results from this study indicated that the level of indigenous Pro in rice seedlings is quite sensitive to Cr(III) stress under different N sources, and mathematical modeling showed a reliable result to estimate the relationship between Pro content and N source application in rice plants in response to Cr(III) exposure .