Based on the threshold effect model and by applying threshold regression method proposed by Hansen, with the panel data of Xinjiang area during 2004—2013, and using farmer and herdsmen’s net income as threshold variable, the paper empirically analyzes the threshold effect of the relationship between famers’ income and agricultural input-output. The empirical result shows that famer and herdsmen’s per capita net income has a significant impact on the agricultural input-output, and that there is prominent threshold effect. When the famer and herdsmen’s per capita net income is more than the threshold value of 8050 yuan, the output elasticity brought by the sown area of the crops, the agricultural electricity consumption and the effective irrigation area will increase. When the famer and herdsmen’s per capita net income is more than the threshold value of 9650 yuan, the output elasticity brought by the total power of agricultural machinery will increase. The paper verifies that the per capita income of farmer and herdsmen will raise agricultural output in Xinjiang. Famer and herdsmen’s per capita net income in southern Xinjiang autonomous region has a certain distance from the threshold value, which restricts the further rise of agricultural output elasticity. Therefore, it’s important to promote farmer and herdsmen’s net income in southern Xinjiang and to mainly support this region.