Le Clos posted a time of 49.14 in the 100m butterfly to beat Takeshi Kawamoto (Japan) and Pavel Sankovich (Belarus), respectively.
He has won all four 100m butterfly events so far this season.
Le Clos also took part in the 50m freestyle race in which he took silver behind winner Vladimir Morozov of Russia who clocked the best time in 20.88 seconds. Great Britain’s Ben Proud completed the podium.
South Africa's Myles Brown grabbed the first men’s gold medal at stake on day two in Dubai in the 200m free (1:43.11), giving South Africa a third gold medal and then a fourth one with a win in the 1 500m in 14:46.49.
Hurley maintained his winning pace by clocking the best time in the 200m back in 1:52.53.
Japan’s Daiya Seto was the best in the 200m IM (1:52.41), narrowly beating Germany’s Philip Heintz and Josh Prenot (USA).
Seto collected his sixth gold medal in this event at the World Cup on Wednesday night. Heintz had won the three first races of the season, while a Chinese athlete, Wang Shun, took gold in the fourth one (Beijing).
Hungary’s Katinka Hosszu, meanwhile, maintained the form which saw her win four events on day one in Dubai to win another five races on day two.
Over the two-day competition the swimming star collected 12 medals, nine of which were gold as well as four silver medals.
In addition to Hosszu’s exploits in Dubai, Zsuzsanna Jakabo was in great shape and added to Hungary’s pride with four silver medals as well as a bronze. Gergely Guyrta also gave Hungary a medal, with bronze in the 1 500m.