At Cornell, Henley's research was in the theory of frustrated magnetism, both classical and quantum; interacting electron systems; quasicrystals; and biological physics.

In interacting electron systems, Henley's research group worked on the border of analytic theory and computation. They studied the ground states of a spinless fermion lattice model with supersymmetry. They also worked on phenomenology of scanning tunneling microscopy measurements in high-temperature superconductors.

In biological physics, Henley led projects in pattern formation and mechanics, specifically a large project about the physical bases of left/right symmetry breaking in various animals including snails; in plants; or in assemblies of single cells. He also was fascinated by the exterior shell geometry of viruses and worked to model the mechanics of plant roots.