In 2020，under the impacts of intensified international political conflicts and COVID-19，the innovation and development of the five traditional special economic zones has slowed down，leaving huge room for improvement in general. After combing and analyzing，this report mainly draws the following conclusions：the rise of local government debts has a significant negative impact on the investments by the whole society in innovation and development；an excessively high proportion of investment in basic research will squeeze the resources of innovation and development to some extent，thereby affecting the performances of innovation and development. Based on this，this report suggests that special economic zones should pay more attention to the balance between policy orientation and market orientation in the process of innovation and development，and establish a sound and sustainable innovation input system.