Judging by pure numbers, Marsh "won" the Bone Wars. Both scientists made finds of immense scientific value, but while Cope discovered a total of 56 new dinosaur species, Marsh discovered 80. In the later stages of the Bone Wars, Marsh simply had more men and money at his disposal than Cope. Cope also had a much broader set of paleontological interests, while Marsh almost exclusively pursued fossilized reptiles and mammals.
Several of Cope's and Marsh's discoveries are among the most well-known of dinosaurs, encompassing species of Triceratops, Allosaurus, Diplodocus, Stegosaurus, Camarasaurus and Coelophysis. Their cumulative discoveries defined the then-nascent field of paleontology; before Cope's and Marsh's discoveries, there were only nine named species of dinosaur in North America. Some of their ideas—such as Marsh's argument that birds are descended from dinosaurs—have been upheld; while others are viewed as having little to no scientific merit. The Bone Wars also led to the discovery of the first complete skeletons, and the rise in popularity of dinosaurs with the public. As paleontologist Robert Bakker stated, "The dinosaurs that came from [Como Bluff] not only filled museums, they filled magazine articles, textbooks, they filled people's minds."
Despite their advances, the Bone Wars also had a negative impact not only on the two scientists but also on their peers and the entire field. The public animosity between Cope and Marsh harmed the reputation of American paleontology in Europe for decades. Furthermore, the reported use of dynamite and sabotage by employees of both men may have destroyed or buried hundreds of potentially critical fossil remains. Joseph Leidy abandoned his more methodical excavations in the West, finding he could not keep up with Cope's and Marsh's reckless searching for bones. Leidy also grew tired of the constant squabbling between the two men, with the result that his withdrawal from the field marginalized his own legacy; after his death, Osborn found not a single mention of the man in either of the rivals' works. In their haste to outdo each other, Cope and Marsh haphazardly assembled the bones of their own discoveries. Their descriptions of new species, based on their reconstructions, led to confusion and misconceptions that lasted for decades after their deaths.
A 2007–2008 excavation of several of Cope's and Marsh's sites suggest that the damage perpetrated by the two paleontologists was less than what has been reported. Using Lakes' field paintings, researchers from the Morrison Natural History Museum discovered that Lakes had not actually dynamited the most productive quarries in Colorado; rather, Lakes had just filled in the site. Museum director Matthew Mossbrucker theorized that Lakes propagated the lie "because he didn't want the competition up at the quarry—playing mind games with Cope's gang."
- Besides being the focus of historical and paleontological books, the Bone Wars was the subject of the graphic novel Bone Sharps, Cowboys, and Thunder Lizards, by Jim Ottaviani. Bone Sharps is a work of historical fiction, as Ottaviani introduces the character of Charles R. Knight to Cope for plot purposes, and other events have been restructured
- The Bone Wars was one of three stories retold in the "New Jersey" episode of the Comedy Central series Drunk History. Cope was portrayed by Tony Hale and Marsh by Christopher Meloni, with Mark Proksch as the drunk storyteller.
- The 2016 young adult novel, Every Hidden Thing by Kenneth Oppel, features the fictional children of Cope and Marsh as they live their own Romeo and Juliet style adventure in the midst of the Bone Wars.
- In 2016, HarperCollins Publishers announced the release of a previously unknown novel by Michael Crichton, Dragon Teeth, the manuscript for which was discovered by his widow. In the novel, a fictional apprentice to both Cope and Marsh makes his own historic discovery.