Cross Island NWR is a complex of six islands (Cross, Scotch, Outer Double Head Shot, Inner Double Head Shot, Mink, and Old Man Islands) that encompasses 1,700 acres in the town of Cutler. Cross, Mink, and Scotch islands are covered predominantly by spruce-fir forest and supports a variety of small mammals, white-tailed deer, bald eagles, ospreys, and song birds. A large salt marsh is located on the western end of Cross island. During the fall, thousands of waterfowl, songbirds, shorebirds, and raptors pass through on their southward migrations. The Double Head Shots and Old Man Islands are covered predominantly by grasses and shrubs and are used by nesting seabirds. Old Man Island is one of only four nesting sites for razorbills in the Gulf of Maine.

The varied topography of Cross Island includes hills, bays, inlets, high sea cliffs, and several cobble beaches scattered along all but its rugged south shore. Vegetation on the island is dominated by dense stands of red and white spruce, balsam fir, yellow and paper birch, and red and striped maple. Several grassy opening and wetlands support a diversity of plant and wildlife species. Botanical species of note include livid sedge and coast blite goosefoot, both State-listed threatened species, and maritime slope bog, a rare plant community. A pair of threatened bald eagles has nested on the island in recent years.

The vegetation on Mink and Scotch Island is dominated by red spruce and balsam fir. Bald eagles have recently nested on Mink Island, and it is believed that the same breeding pair of eagles has also nested on Outer Double Head Shot and Cross Islands. The vegetation on Outer and Inner Double Head Shot Islands is divided between red spruce and balsam fir on the northern portions of the islands, and mixed grasses dominating the southern portions of the islands. Herring and great black-backed gulls, Leach's storm petrels, and common eiders nest on the islands. Old Man Island is dominated by granite ledges and sea stacks. Vegetation on the island is sparse. This island is one of only seven islands in the Gulf of Maine to support nesting razorbills.

Inter-tidal wetlands surrounding the six islands within Cross Island NWR provide extensive foraging opportunities for a variety of breeding, migratory, and wintering species. Spring and fall migrations draw flocks of waterfowl, particularly American black ducks, blue and green-winged teal, common goldeneye, bufflehead and long-tailed ducks. Raptors and songbirds also use the islands to rest and feed during migration. Shorebirds feast on invertebrates in the saltmarshes and mud flats, putting on fat to carry them on their long flight to South America.

The Refuge was acquired in 1980, and is now managed as part of Petit Manan National Wildlife Refuge Complex.

Like many of the islands on the Maine coast, islands within the Cross Island NWR have a long history of human habitation. Known by the Native Americans as Sebohegonet, Cross Island was for generations used as a base for fishing operations. Later, early mariners also used the island as a base for their fishing activities. In the latter half of the 19th century, Cross Island supported several saltwater farms and even a small village with a school and store.

The U.S. Lifesaving Service built a lifesaving station on Cross in 1874, which became a Coast Guard station in 1928. The Coast Guard soon abandoned the old lifesaving station, and built a new station at Northeast Harbor in the 1930's. Prior to Service acquisition, the island also had an extensive history of commercial timber harvesting and commercial hunting operations.