Flogging Molly's music is influenced by bands such as The Pogues, The Dubliners, Stiff Little Fingers, and The Clash. Dave King says the Pogues were a huge influence. The album Within a Mile of Home is dedicated to Joe Strummer and Johnny Cash.
Their music ranges from boisterous celtic punk, like the pirate-themed "Salty Dog", "Cruel Mistress", and "Seven Deadly Sins", or the defiant "What's Left of the Flag", "Drunken Lullabies", and "Rebels of the Sacred Heart" to more sombre songs like "Far Away Boys", "The Son Never Shines (On Closed Doors)", and "Float." Lyrics typically touch on subjects such as Ireland and its history, drinking, politics, love, and include several references to the Roman Catholic Church.