This paper uses panel cointegration approach to estimate the agricultural total factor productivity (TFP) from 30 regions from 1978 to 2004 in China. The results of panel unit root find that all inputs and output variables are nonstationary series. Pedroni (1999) panel cointegration tests present the evidence supporting the existence of the long run cointegration relationship. This paper finds the estimator of FMOLS is better than OLS and DOLS. Agricultural total factor productivity is estimated based on Kao and Chiang (2000) panel coefficients estimation.