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HOUSTON, Oct 2 (Reuters) - ConocoPhillips (COP.N: Quote, Profile, Research), the third-largest U.S. oil company, said on Thursday the hurricanes that swept through the Gulf of Mexico in the third quarter hurt operations at its refineries and weighed on its oil output.

The storms curtailed Conoco's output by about 20,000 barrels of oil equivalent per day, putting its quarterly production at flat to slightly below the second-quarter level.

In the second quarter, Conoco reported production of 1.8 million BOE per day, excluding output from its 20 percent owned Russian affiliate Lukoil (LKOH.MM: Quote, Profile, Research).

A decline in global refining margins versus the second quarter was partially offset by an increase in marketing margins, the Houston company said.

Hurricanes Gustav and Ike battered the energy sector during the quarter, shuttering 16 refineries that represent 25 percent of the nation's capacity.

Conoco said the storms cost its refining and marketing arm about $200 million after taxes.

Refining margins on the Gulf Coast rose in the quarter, but storm-related shutdowns "significantly limited the company's ability to capture this margin increase," Conoco said in its interim third quarter report.

Earlier this week, Conoco said its Gulf Coast refineries have returned to normal. The company had shut its 247,000 barrel per day Alliance and 239,000 bpd Lake Charles refineries, which are both in Louisiana, due to the storms.