A detailed understanding of the corneal biomechanical response is an important prerequisite to understanding corneal diseases such as keratoconus and for placing the empirical equations used in refractive surgery on a physical basis. We have assembled a combined nonlinear optical microscopy (NLOM) and optical coherence microscopy (OCM) imaging system to simultaneously capture coregistered volumetric images of corneal morphology and biochemistry. Fudicial markers visible in the OCM volume enabled the calculation of strains for multiple depth layers in rabbit cornea. The results revealed a depth dependent strain distribution, with smaller strains in the anterior stroma and larger strains in the posterior stroma. The stress-strain curves can be grouped readily by depth into three groups: anterior (∼20%), transitional mid (∼40%), and posterior (∼40%). Cross-sectional images of collagen lamellae, visible in NLOM, showed inhomogeneous collagen structure and its response to intraocular pressure along the anterior-posterior direction. The inhomogeneities correlate well with the noted heterogeneous corneal mechanical properties. The combined NLOM-OCM system can measure corneal microstructure and mechanical response uniquely, thus providing a microstructural understanding of corneal response to changes of collagen structure.