James will win his 44th cap at Murrayfield and comes in to the side after Gethin Jenkins failed to recover from a calf injury picked up in the victory to Italy.
Jones and Warburton, who both featured from the bench in Rome after recovering from injuries, start in the second row and at openside flanker respectively.
Ryan Jones (Ospreys) who has led Wales to two successive away victories will again captain the side and will line up in the back-row alongside Warburton and Toby Faletau (Dragons) at No 8.
Alun Wyn Jones comes into the second row to partner regional team-mate Ian Evans and in the front row James comes in to play alongside Ospreys duo Richard Hibbard and Adam Jones.
Wales and Scotland go into Saturday's match level on points in the RBS 6 Nations table with two victories apiece and the visitors will be looking for their fifth successive away victory in the tournament, a feat they haven't achieved before.
For the fourth match running, interim head coach Rob Howley has named an unchanged back line.
Mike Phillips (Bayonne) will continue his partnership at half-back with Ospreys fly-half Dan Biggar with Jamie Roberts (Blues) and Jonathan Davies (Scarlets) named in the centre.
Leigh Halfpenny (Blues), Alex Cuthbert (Blues) and George North (Scarlets) make up the back three.
"We have had two good, hard fought away victories but we know will have to be at our best again to come away from Murrayfield with the result," said Wales interim head coach Rob Howley.
"It's disappointing for Gethin to miss out but Paul has impressed and made an impact in each game he has played.
"We are bringing in a wealth of experience with Alun Wyn and Sam and they both performed well off the bench in Rome.
"Ryan has led the team to two wins and deserves to captain the side against Scotland.
"We have spoken a lot about momentum in this tournament and we go into the game with two wins under our belt but Scotland are in the same position and it's going to be a good challenge."
There are three changes on the replacements bench. Blues prop Scott Andrews comes into the match day squad to replace Paul James and Andrew Coombs and Justin Tipuric take their place amongst the replacements.
WALES: Leigh Halfpenny; Alex Cuthbert, Jonathan Davies, Jamie Roberts, George North, Dan Biggar, Mike Phillips; Paul James, Richard Hibbard, Adam Jones, Alun Wyn Jones, Ian Evans, Ryan Jones (capt), Sam Warburton, Toby Faletau.
REPLACEMENTS: Ken Owens, Scott Andrews, Craig Mitchell, Andrew Coombs, Justin Tipuric, Lloyd Williams, James Hook, Scott Williams.