Abstract This paper presents large-area profile measurement of ultra-precision diamond turned sinusoidal surfaces by using a specially developed scanning tunneling microscopy (STM). The new prototype of STM system employs a long stroke PZT servo actuator as the Z-directional scanner, an integrated capacitance displacement sensor to accurately measure the Z-directional profile height, a motorized stage with long traveling stroke for carrying out large-area scanning. A simple method for self-calibration of the inevitable sample tilt is proposed in order to achieve large-area measurement without tip-crashing or losing of tip-sample interaction. Several types of ultra-precision machined sinusoidal freeform surfaces with different geometrical parameters are measured by the new STM system over large scanning areas at the scale of millimeters. Specially, a sinusoidal surface with peak-valley amplitude of 22 μm and periodical wavelength of 550 μm is successfully measured and imaged by the STM system. The measurement repeatability error, repeatability standard deviation and measured profile deviation are also evaluated. It is confirmed that the new STM system is capable of carrying out large-area as well as large-amplitude measurement of the ultra-precision machined sinusoidal surfaces.