This article studies the effect of mirror misalignment on run‐out overlay errors in a synchrotron radiation based x‐ray lithography system. Using the ES‐5 beam‐line installation at the CXrL as an example, we found that the current beamline mirror alignment method, which relies on the final beam shape and orientation at the mask‐wafer plane, is insensitive to the mirror grazing incident angle alignment. Simulations using the ray‐tracing programshadowindicate that a smaller than ±0.5‐mrad mirror grazing angle misalignment consumes the required run‐out overlay error budget of the beamline. A direct beamline run‐out overlay measurement technique based on the Hartmann method was developed for the beamline mirror alignment. This measurement technique was applied to our ES‐5 beamline mirror alignment procedure. The measurement results show that the beamline induced run‐out error of the installed ES‐5 beamline is less than 0.014 μm in both horizontal and vertical direction for a 25‐mm exposure field with a mask‐wafer gap of 40 μm. The across field run‐out error distribution is also compared withshadowsimulation results. The good agreement between measurement and simulation data indicates that our measurement technique provides a sensitive, practical, and accurate method for x‐ray lithography beamline mirror alignment and evaluation.