Magnetically coupled resonant (MCR) wireless power transfer (WPT) is a promising technology, which has been widely used in many practical applications. In the practical application environment the misalignments between the transmitting coil and the receiving coil can not be avoided, and it will cause a rapid decline in transmission efficiency. So the misalignments have limited the applications of MCR-WPT technology in many fields. The mathematical formula of transmission efficiency with angular misalignment and lateral misalignment was deduced. And the effects of angular misalignment and lateral misalignment on the transmission efficiency were researched by simulation experiments. And the changing regularity of the transmission efficiency with the change of the angular misalignment and lateral misalignment was obtained. The results show that when there is an angular misalignment between the transmitting coil and the receiving coil, the transmission efficiency can be optimized by adjusting the lateral misalignment between the coils. And when there is a lateral misalignment between the coils, the transmission efficiency can be optimized by adjusting the angular misalignment between the coils. An experimental prototype of MCR-WPT system was built, and experiments had been carried out to evaluate the accuracy of the theoretical analysis. Therefore, the study in this paper lay a theoretical foundation for the analysis of WPT in the complex environment, and also provide a useful reference for the design of WPT system.