Ovidio Limon Sanchez was captured by soldiers in Culiacan - the capital of Sinaloa state on the Pacific coast.
He is accused of organising huge shipments of cocaine into southern California and of running a network that distributes it throughout the US.
He faces extradition to the US, which had offered a reward of up to $5m (£3.13m) for his arrest.
Mr Limon Sanchez is alleged to be a close ally of Joaquin "El Chapo" Guzman, the fugitive leader of the Sinaloa cartel, who is Mexico's most wanted drug lord.
"The detention of Limon Sanchez significantly affects the Guzman criminal organisation in its capacity to traffic cocaine and weakens its ability to generate financial resources," defence ministry spokesman Col Ricardo Trevilla said.
He was captured by the Mexican army "without a shot being fired", Col Trevilla added.
Mr Limon Sanchez allegedly smuggled tons of cocaine into southern California and brought back millions of dollars to Mexico in cash shipments, according to a notice on the US State Department website.
He is the latest in a series of alleged top drug traffickers to be killed or captured in Mexico since President Felipe Calderon began deploying the military to fight the cartels in 2006.
But critics of his policy say these successes have not slowed the flow of drugs and may have exacerbated the violence by triggering power struggles within the cartels.