Information of the entire cylindrical inner surfaces can be achieved by using a Fizeau interference system and a 90° conical mirror in a one-time measurement. In order to achieve high-precision surface measurement, the alignment of experimental apparatus is very crucial. However, defects of the alignment may cause the spatial orientation of the cone mirror and the tested cylinder difficult to determine, and any misplacement from ideal location may result in large measurement errors. Therefore, to remove the system errors, the reasons of all kinds of misalignment should be well understood and their influences on the measurement results should be analyzed. By establishing the mathematical model in cylindrical coordinate, the change formula of offset error and rotational error is deduced. The formula is verified by numerical simulation of Matlab software and practical measurement. The results show that the misalignment error coefficient can be successfully derived with the proposed formula, which will further benefit system error correction.