Digital holographic microscopy (DHM) is a successful technique frequently used to assess the phase in imaging experiments. Combining DHM with nonlinear generation opens the possibility of measuring phases in nonlinear processes such as high-harmonic generation and characterizing nanostructures with an increased sensitivity. In this paper, we demonstrate that the combination of DHM and harmonic generation from solids can be used to reliably perform 3D reconstructions of samples and also investigate structural parameters of subwavelength periodic structures with improved accuracy. We were able to discriminate gratings etched in silicon, with only a few tens of nanometers change in critical dimension, down to a pitch of 400 nm, which is well below the wavelength of the near-infrared (NIR) probing laser source. This technique can in principle be used with all high-harmonic-emitting materials and is expected to reach even larger gains in resolution by probing higher-order harmonics. These results pave the way for sensing of subwavelength structures via nonlinear light generation, for instance, in the semiconductor industry.