WASHINGTON—The commander in charge of U.S. military operations in the Pacific wants Congress to give the command more money for defense programs to counter China, reflecting his concerns that the Pentagon’s budget isn’t realigning quickly enough to address the threat from Beijing.

Adm. Phil Davidson, the head of U.S. Indo-Pacific Command, believes the Defense Department’s fiscal 2020 budget doesn’t include enough funding to provide “immediate and necessary resources” for the region he oversees, according to a letter he wrote...