The Australian, who won gold in the time trial in Rotterdam on Saturday, completed a superb weekend by regaining the title he won in 2012.
Willoughby - a silver medallist at the 2012 Olympic Games in London - beat Tory Nyhaug of Canada to gold at the Ahoy Arena.
Great Britain's Tre Whyte rounded off the top three, reacting quickest to take the bronze after being caught up in a five-man crash.
Whyte's compatriot Liam Phillips suffered disappointment in his quest to retain the world title, crashing out in the 1/8 finals, while Olympic champion Maris Strombergs was eliminated in the semi-finals.
Meanwhile, in the women's elite race there was delight for Colombia's Mariana Pajon.
Olympic champion Pajon reclaimed the title she won in 2011 by beating American Alise Post to the line in a race that did not feature 2013 winner Caroline Buchanan after the Australian was knocked out in the last four.
Home hope Laura Smulders capped off a successful competition by winning bronze on the back of her triumph in the women's time trial.