Electron beam lithography (EBL) is an important lithographic process of scanning a focused electron beam (e-beam) to direct write a custom pattern with nanometric accuracy. Due to the very limited field of the focused e-beam, a motion stage is needed to move the sample to the e-beam field for processing large patterns. In order to eliminate the stitching error caused by the existing “step and scan” process, we in this paper propose a large range compliant nano-manipulator so that the manipulator and the e-beam can be moved in a simultaneous manner. We also propose an optimized design of the geometric parameters of the compliant nano-manipulator, so that the dimensions and rotational stiffness are suitable for EBL applications in a vacuum environment. Experimental results demonstrate 1 mm × 1 mm travel range with high linearity, ∼0.5% cross-axis error and 5 nm resolution. Moreover, the high natural frequency (∼56 Hz) of the manipulator facilitates it to achieve high-precision motion of EBL.