Having finished first and fifth in the respective races on Saturday, the 27-year-old again clocked the fastest time in the 500m ahead of Australia's Daniel Greig and Japan's Keiichiro Nagashima.
While in the second 1000m race, he moved up to finish third behind Denis Kuzin of Kazakhstan and USA's Shani Davis.
It meant Mulder finished with an overall total of 139.885 points, the sixth time a Dutchman has taken a World sprint title.
Davis was second on 140.600 points, while Greig became to first Australian to medal an ice championships since Steven Bradbury's short track gold in 2002 when he took bronze.
In the women's contest, 2012 champion Yu Jing added another 500m win to that achieved on Saturday to regain her title ahead of fellow Chinese skater Hong Zhang in second.
Having also finished fourth in the second 1000m, the Chinese speed skater equalled compatriot Ye Quaibo's record of two World Cup Sprint titles with a score of 151.275.
Heather Richardson, winner of the 1000m and third in the 500m races on Sunday, took the bronze with 151.790 points, while Zhang finished with 151.705 points for second.