There is still controversy over the source of agriculture total factor productivity (TFP) growth, but the impact of reform of agricultural factor market-oriented allocation over the past 40 years has been ignored. By adopting the transcendental logarithmic production function stochastic frontier model, the TFP growth of maize in China from 1978 to 2018 has been calculated. The technological progress, the technological efficiency change, the scale efficiency change, and the allocation efficiency change has been studied, so as to explore the source of TFP growth and its regional differentiation. The results show that the average annual growth rate of TFP of maize in China was 1.38%. The growth rate in Southwest and North China was high while that in Northeast was low. The reform of factor market-oriented allocation promoted the allocation efficiency and was the important source of growth of TFP of maize. The effect of technology progress was increasingly obvious while the technology efficiency didn’t improve significantly. Scale efficiency declined and didn’t help to promote TFP growth.