During his time at Oberlin, Bowen did some research on the properties of steel for the scientist Robert Hadfield.

Bowen gave lectures on general physics at Caltech and did research on cosmic rays and followed his studies on UV spectroscopy.

With that data and the inspiration from a chapter on gaseous nebula and the emission of radiation at low density in the book Astronomy by Henry Norris Russell, Raymond Smith Dugan and John Quincy Stewart he achieved his best known discovery.

The green emission lines of the Cat's Eye Nebula at 4959 and 5007 Ångström were discovered by William Huggins in 1864.

Bowen was able to calculate the forbidden transitions of doubly ionized oxygen to be exactly where the lines had been found.