The Middle East and North Africa countries are important partners of the Belt and Road Initiative. The economic development level and institutional environment of the countries in the region are very different, and there are great differences in economic system and political system between MENA and China. This paper calculates the political institutional distance and economic institutional distance between China and the MENA’s 24 countries based on the data related to the Global Governance Index and the Economic Freedom Index, and makes an empirical analysis of the impact of bilateral institutional distance on China’s export trade and its export trade potential to the region through Gravity Model by using the data of China’s export trade to the region from 2007 to 2016. The results show that there is a threshold to make the bilateral institutional distance have a negative effect on China’s export trade to the region. In addition, we know that China still has great potential for export trade to some countries in the region through the measurement of trade potential. More discussions and some suggestions on how to reduce bilateral institutional differences are put toward at the end.