Russian Denis Yuskov earned gold, while Koen Verweij of the Netherlands took home bronze.
Morrison is coming of a successful Sochi Olympics in 2014, winning silver and bronze in the 1,500m and 1,000m events, respectively.
Brittany Bowe led an American one-two in the 1,000m, beating teammate Heather Richardson into second.
A year after a disastrous showing by the U.S. speedskating team at the Sochi Olympics, the Americans dominated at the Thialf oval.
Richardson set a new track record of 1 minute, 14.49 seconds in her pairing against defending champion Olga Fatkulina of Russia only to see Bowe shatter it again with her winning time of 1:13.90. Karolina Erbanova of the Czech Republic was third.
Bowe said her entire season had been focused on the race.
She said: "Since the beginning of the year, my goal has been world single distance championships gold medal in the 1,000."