Nelly in a big mess,drugs and a pistol discovered on his bus.

We're told cops pulled the bus over -- and after performing a search, they found 36 small baggies of heroin (totaling .64 ounces) and over TEN POUNDS of marijuana inside a large green duffel bag (an amount roughly the size of a large bed pillow).

Cops also say they found a loaded .45 caliber pistol.

There were seven people riding on Nelly's bus at the time -- including the rapper -- and they were all detained during the search.

According to law enforcement sources, one of the passengers -- a guy named Brian Keith Jones -- admitted the drugs and the gun were his. He was subsequently placed under arrest.