Exchange rate fluctuation and misalignment are important factors affecting international trade. This paper uses Behavioral Equilibrium Exchange Rate (BEER) model to measure RMB exchange rate misalignment from 1994 to 2018. Meanwhile, based on the Standard Classification of International Trade (SITC), this paper selects the annual data of 10 categories of import and export industries in the same period in China to study the impact of RMB exchange rate misalignment on imports and exports of different industries with Autoregressive Distribution Lag(ARDL) Model and Error Correction Model(ECM). It is found that the real effective exchange rate of RMB slightly misaligned. The impact of RMB exchange rate misalignment on import and export industries is heterogeneous and has different time lag effects. On the whole, the impact of exchange rate misalignment on import is greater than that on export, and the impact of long-term exchange rate misalignment on import and export is greater than that of short-term exchange rate misalignment and the direction of the influence of the two on import and export is not entirely the same among different industries and in different periods of time. Therefore, it is suggested to construct and improve the long-term mechanism and emergency mechanism of RMB exchange rate management, to develop diversified exchange rate risk hedging tools, and to implement differentiated import and export industry development strategies and enterprise exchange rate risk management strategies.