Omar Martin Estrada - known as El Kilo - is accused of being the local chief of the drug cartel Zetas in San Fernando, where the bodies were found.
A $1. 2 m (￡ 735,000) reward had been offered for his arrest.
It is believed that most of the victims have been removed from the bus.
Mr. Estrada is also accused of being involved in the murder of 72 migrants Central and South America, whose bodies were found in the same area last year.
Five other suspects were also arrested.
The security forces had already arrested at least 16 suspected members of the Zetas in relation to mass graves.
They also questioned 16 local police charged with protecting the criminals.
It is believed that most of the victims have been removed from the intercity bus travelling north to the American border.
The motive for the murders is not clear, but there is speculation that the cartel gunmen may have killed men who refused to join their ranks.
MissingSan Fernando near the border with American is one of the deadliest places in the Mexico drug war, says the BBC Julian Miglierini in Mexico City.
It is believed that the Zetas and their former allies, the Gulf cartel, are fought for control of the region because it is a route for illicit drug trafficking to the United States, our correspondent adds.
Forensic scientists have worked to identify the bodies, which some have been taken to Mexico City.
Hundreds of people whose parents disappeared went to see if they can identify the members of their families among the dead.
The Mexican Government, said about 35,000 people have been killed in violence related to the drug since President Felipe Calderón began deploying troops to fight the cartels in December 2006.
More than 5,000 people have been reported missing, according to the Mexico human rights commission.
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