The topography of San Miguel Islands is quite low in contrast to the rugged peaks, ridges and canyons found on some of the larger islands. Waters surrounding the islands are often rough and hazardous due to submerged rocks and shoals. Prevailing northwesterly winds are almost constant, blowing sand quite readily. Dense fog often shrouds the island from view. It is the least accessible of the four Northern Channel Islands, and has been called the "graveyard of the Pacific" due to the large number of shipwrecks. The highest point on San Miguel Island is Green Mountain rising 831 feet at its highest point. Prince Island, a small islet at at the mouth of Cuyler's Harbor is 39.4 acres and has an elevation of 296 feet.

San Miguel Island is composed of Tertiary rocks and Pleistocene terrace deposits. In addition, Eocene marine sediments are present on the western part of the island, Miocene volcanic rocks are confined to the eastern part.

There is an extensive, very well developed caliche forest on San Miguel Island. It offers good evidence that the island once supported large trees and shrubs, unlike today. This is the most spectacular caliche to be found on any of the California Channel Islands.