Rutherford, who has also won world, European, and Commonwealth golds, was given a host-nation place for the event after winning the British indoor title, and subsequently competed in the Müller Indoor Grand Prix in Glasgow on Sunday.
However, the 31-year-old has decided not to take part at the worlds in order to retain full fitness in time for the outdoor season.
“My performance from the British Championships to the Indoor Grand Prix in Glasgow at the weekend showed improvement but it was still not at the level I demand of myself,” said Rutherford, who competed just three times in 2017 and underwent groin and ankle surgery.
“It has not been an easy decision, but I have therefore chosen to withdraw from the world indoor championships. I am now going to take a few days to recover from Glasgow before resuming training as I prepare for a successful summer.”
“I am committed to becoming the first long jumper to win three European titles in a row and will be training hard over the coming months to return to the track as fit as ever.”
British Athletics performance director Neil Black said Rutherford had made significant progress since returning to competition.
“Unfortunately, that progress is not quite enough for him to be able to compete at the high standards he demands in Birmingham,” he said.
The world indoor championships take place in Birmingham on March 1-4.