Maury, who was born at Cold Spring-on-Hudson, New York, came from a family with a distinguished scientific background. She was a cousin of Matthew Maury, the oceanographer, a niece of Henry Draper, the physician and astronomer after whom the Harvard star catalog was named, her sister became a paleontologist, while her father, a clergyman, was also a well-known naturalist. She herself was educated at Vassar, graduating in 1887, and in 1889 became an assistant to Edward Pickering at Harvard College Observatory. There she worked alongside an unusually large collection of women astronomers of whom the most eminent were Annie Cannon and Henrietta Leavitt. Apart from the years 1899–1908, when she lectured at various eastern colleges, she retained her position at Harvard until her retirement in 1935.

Much of her work was on the classification of stellar spectra for the Harvard catalog. At about the same time that Cannon was revising the system of spectral classification of stars, Maury proposed an additional modification that turned out to be of permanent significance. It was important to notice, she argued, not just the absence or presence of a particular spectral line but also its appearance. Stars with normal lines she marked ‘a’, those with hazy lines ‘b’, and those that were sharp she marked ‘c’; intermediate cases were marked ‘ab’ or ‘ac’. This has been described as the first step in using spectroscopic criteria for the luminosities of stars. Maury's spectral classifications, including those of 681 bright northern stars, were published in 1896 in the Harvard Annals. Ejnar Hertzsprung was quick to see the significance of her classification system and in 1905 pointed out that c-type and ac-type stars were brighter than a- or b-type stars and were in fact giants.

Maury spent many years studying and detecting spectroscopic binary stars and as early as 1889 had determined the period of Mizar, in Ursa Major. This was the first spectroscopic binary to be discovered, identified by Pickering earlier in the year. The two stars in a spectroscopic binary cannot be resolved visually but as they revolve they will each alternately approach and recede from an observer on the Earth. This causes an alternate lengthening and shortening of the emitted light waves and will produce a periodic doubling of the spectral lines. Maury's particular interest was the binary Beta Lyrae, the investigation of which she continued long after her retirement.