Income from non-agricultural industries operated by rural households is an important income source of farmers’ income. According to the Regional Rural Residents’ Net Income Per Capita in 2004 issued by the State Statistics Bureau and the relevant statistics of national comprehensive investigation(CGSS2005) in 2005, the impacts of farmers’ income gap and farmers’ individual features on their income and the impacts of income from non-agricultural industries operated by rural households on farmers’ individual income differences are analyzed by applying Hierarchical Linear Models (HLM) as an analysis tool to establish the null model of HLM, excluding the second level model of the second level prediction variables and including the second level model of the second layer prediction variables. The analysis assumes that farmers’ individual income varies hugely in different provinces; farmers’ individual income has close relation with farmers’ individual features; the improvement of income from non-agricultural industries operated by rural households has different impacts on farmers’ income.