From the perspective of total factor production efficiency of ports, the traditional data envelopment analysis(DEA)method is improved by using the Malmquist total factor productivity index, which overcomes the shortcomings of the traditional DEA method that cannot deal with different periods. The DEA Malmquist model with variable returns is established so as to investigate the upgradation degree and the development trend of transformation of ports. It is used to analyze the coastal ports in Shandong Province. The results show that the overall efficiency of coastal ports in Shandong Province has an increasing trend from 2014 to 2018. The development situations of various ports are not balanced. Although the Malmquist productivity index of the coastal ports in Shandong Province is restricted by the scale efficiency, it still has an increasing trend. Some suggestions are put forward for the transformation and upgradation of coastal ports in Shandong Province.