This paper constructs the global Malmquist-Luenberger productivity index based on global production technology set, and then applies the index to estimate the total factor productivity and its components of China’s rural commercial banks during 2008-2013 under the constraint of non-performing loans, and examines its convergence. The results show: the average total factor productivity for the China’s rural commercial banks decrease slightly with a fairy significant decrease in technical change. The change trajectory of productivity growth for rural commercial banks in eastern region shows V shape, the opposite is true in middle and west region. The property right reforms have an active effect on improving the technical efficiency, the monetary policy, new regulation standard and industry transfer policy have negative effect on technical progress. The total factor productivity of China’s rural commercial banks shows unconditional and conditional β convergence, the increase of intermediary business technical content and real GDP growth rate can promote the productivity growth of China’s rural commercial banks.