It will remain official beer supplier to the Old Trafford organisation until 2015.
The Penny Street firm and Blackburn Rovers announced last month that their arrangement had come to end with Dutch-company Heineken taking over the supply of Ewood Park’s bars.
Thwaites remains the official supplier to Burnley Football Club and its Turf Moor bars.
Blackburn MP Jack Straw said: “It’s wonderful news that Thwaites are continuing to sponsor Lancashire County Cricket Club as they do Burnley FC.
“It is sad that Thwaites and Blackburn Rovers could not come to an agreement to supply of its beers to Ewood Park.”
Thwaites, first sponsored Lancashire in 2005 and started supplying beers to its Old Trafford ground in 1995.
As part of the agreement, the Thwaites Wainwright logo will appear on club shirts for the next three seasons.
Thwaites marketing manager Lee Williams said: “We are delighted to cement our successful and long standing relationship with the club.
“Everyone at Thwaites is hoping Lancashire can build on their dramatic County Championship win of 2011. With the redeveloped Old Trafford also hosting the highly anticipated third Ashes test when England take on Australia it promises to be a summer to savour.”
LCCC business manager, Warren Hegg, said: “We are delighted that Thwaites will continue their association with the club as we embark on an exciting new era.”