We present a 3-D surface profiling method for microlenses that utilizes a Shack–Hartmann wavefront sensor. This method applies to both solid microlenses and liquid–liquid interfaces in liquid microlenses. The wavefront at the aperture stop of a microlens is measured by a Shack–Hartmann wavefront sensor and is then used to calculate the 3-D surface profile of the microlens. Three types of microlenses—a photoresist microlens, a hydrogel-driven tunable liquid lens, and an electrowetting-driven tunable liquid lens—were fabricated and measured. The variable-focus liquid lenses were tested within a wide focal length range. The obtained surface profiles were fitted to spherical and conical surface models to study their geometrical properties. The photoresist microlens was found to be approximately spherical. For the hydrogel-driven microlens, the profile was smooth and nearly spherical at the center but became steep and linear at the aperture edges. The electrowetting-driven liquid lens was also fitted better with the conical model, and its conic constant was determined. The obtained surface profiles were used to estimate the optical properties of microlenses in an optical analysis software package. The comparison between the simulation and experiment results indicated that the accuracy of the estimation is rough and the error could be due to the wavefront measurement and surface fitting approximation.