The Republic of Ireland international scored twice in 13 first-half minutes, before adding a third in injury time to leave Rangers rooted in the relegation zone.
His first saw him beat Robert Green from the edge of the box with his left, before he doubled the home side’s lead with a long-range effort in the 34th minute.
QPR gave hope to their travelling fans when Niko Kranjcar continued a healthy run against the Potters that has seen him score three goals in three games at the Britannia Stadium, his shot sneaking in at the near post after Asmir Begovic parried Charlie Austin’s shot.
It looked like the visitors may get their first away point of the season as they had the majority of the second-half chances, until Walters headed home a minute into injury time to seal his hat-trick.
All of Stoke’s good early work came down the left hand side as Victor Moses linked up well with new defender Philipp Wollschied, and after dominating the early possession it wasn’t long before they scored.
Karl Henry took too much time on the ball and tried to chest it down but when it ran away from him, Stephen Ireland flicked it down and Walters was there to collect and knock it across Green from the left-hand side of the box.
It only took Walters 13 minutes to extend the Potters’ lead with his second. Ireland – who was back in the team after two months out with injury – played the ball across the front of the Rangers defence and the striker was there to put it past Green from outside the box.
Niko Kranjcar continued his good run at the Britannia as he scored his third goal in three games when he halved the deficit in the 36th minute.
Joey Barton ran into the box and squared for Austin who shot, and when Begovic parried his shot away, Kranjcar was there to convert and give the Harry Redknapp something to smile about.
QPR seemed to emerge with more resolve in the second half as they attempted to salvage something from their 11th away trip of the season.
Vargas looked like he was on his way to levelling the scores when he latched on to Leroy Fer’s free-kick and attempted an audacious volley, but Begovic was alert and pushed it over on the hour.
Substitute Peter Crouch nearly scored against his former manager after the Potters found their way back into the game. The lively Ireland tried to smash the ball across the front of the box, but as Crouch stretched for it he sent it wide.
As the game progressed, QPR’s confidence grew and they had the majority of the chances in the second half. Barton won a free kick, which he took himself and the shot bounced off the bar, in front of the goalkeeper and away from goal.
Then a minute into injury-time, Walters headed past Green after Barton’s weak defensive header, sealing his first Premier League hat-trick.
The result leaves Rangers in trouble, a point from safety, while Stoke – despite the absence of the injured Bojan – climb to ninth.
Man of the match: Jonathan Walters.