Linnets' manager Peter Morris blasted his defence following this defeat in Wales.
Despite falling behind to a dubious 52nd-minute free kick the Linnets still looked worth a point after turning in an encouraging performance against the league leaders for the first half of the match.
But in an effort to get back into the game, a double change in personnel by Morris began the demise and the Linnets were sank without trace by the Welsh wizards.
As in last season's fixture, Lynn went into the game with injuries to key players.
Experienced defender Tony Spearing was ruled out of the game due to a back problem while Lee Hudson, clearly still suffering from a knock picked up against VS Rugby, had t be content with a place on the bench.
The signs looked good early on. Richard Skelly's turn and shot scraped the Merthyr woodwork in the eighth minute before Ian Cambridge, making his first staff, forced home keeper Gary Wager into a save two minutes later.
Such was Lynn's first half composure, Merthyr's first chance didn't arrive until the 34th minute when Ian Mitchell sprinted clear of the visiting defence before seeing his shot brush the post with only Lewis to beat.
The home side took the lead seven minutes after the break after Martin Matthews and Jason Pascoe had been harshly accused of bringing down Cohen Griffiths outside the box.
From the resulting Neil Loss free-kick Gareth Abraham headed home. In an instant Lynn amost struck back when Richard Skelly's free-kick was hooked off the line by Mitchell.
It seemed as though The Walks outfit turned their thoughts to the forthcoming FA Cup tie for the final 20 minutes with Merthyr breaking down the defence almost at will.
Darren Porretta scored Merthyr's second following a corner in the 74th minute before the same player set up Mitchell for number three, five minutes later.
Home substitute Sam Bowen scored Merthyr's final goal two minutes later to make it three in six minutes and although Jason Pascoe hit the home bar late on it was a matter of too little too late for Lynn, who were lucky to end the match with a full quota of players on the field.
Captain Colin Hoyle was lucky to escape with only a booking after bringing down Griffiths who was through on goal in the 19th minute and Steve Williams was lucky not to see red after blatantly elbowing Merthyr's David Barnhouse with 15 minutes remaining.
Lynn: Lewis, Matthews, Skelly, Hoyle, Wright (Hopkins 65), Pascoe, Williams (Mead 80), Roberts, McNamara, Cambridge (Hudson 65).
Merthyr: Wager, Barnhouse, Kelly (Bowen 30), Abraham, O'Brien, Gibbins, Porretta, Griffiths, Mitchell, Loss, Clarke. Subs not used: Jenkins, Rivett.