Three goals in the space of seven first half minutes put the hosts on the front foot, before Hall netted either side of the break to complete his hat-trick.
Jay Simpson did pull one back for the O’s on 69 minutes, before Dele Alli added a sixth late on.
Orient made four changes from the side which lost 1-0 at Doncaster Rovers with Shane Lowry, Lloyd James, Jake Taylor and Jay Simpson coming in for Andrea Dossena, Josh Wright, Ryan Hedges and Darius Henderson respectively.
The O’s kicked the game off, but were immediately on the back foot and Rob Hall saw a shot held by Cisak inside the opening minute.
Jobi McAnuff won Orient a free-kick down the left and the ball into the box caused confusion in the Dons penalty area, however, the hosts dealt with the danger and eventually cleared.
Chances were at a premium and Mathieu Baudry did well to deny Will Grigg in the box after the striker had worked his way in from the left with a nice piece of skill to get past Scott Cuthbert.
The hosts had upped the tempo and Kyle McFadzean tried his luck from range and Cisak got down well to palm the effort away and then gather the loose ball at the second attempt.
And they turned that into a goal advantage on 22 minutes when an incise counter attack from the hosts was turned home by Dean Bowditch at the back post.
It got even worse two minutes later as Rob Hall’s shot from the right hand side of the area found its way past O’s goalkeeper Alex Cisak, with Will Grigg putting pressure on the stopper.
Orient found it difficult to regroup and just before the half hour mark Dele Alli was tripped in the box and referee Christopher Kavanagh pointed to the spot.
And Grigg sent Cisak the wrong way to put the hosts 3-0 to the good.
It was going to be an uphill battle, and McAnuff put a dangerous ball into the box, but no-one was able to get on the end of it.
And then an opening was worked for Jay Simpson, however, his fierce shot was well held by Dave Martin in the Dons goal.
But the hosts went further in front on 37 minutes when the ball rebounded into the path of Rob Hall and he fired a fierce dipping shot from 25 yards over Cisak and into the net as the Dons took a 4-0 lead into the half-time interval.
Fabio Liverani made one change at the break with Jake Taylor replaced by Shaun Batt. And in the first minute the O’s created an opening and McAnuff forced a solid save from Martin before the keeper held Batt’s attempt from the rebound.
Jay Simpson saw an effort fall just wide of the target after a mazy run, and up the other end Rob Hall was smartly denied by Cisak after he had jinked his way into the box off the right wing.
But it was to be an occasion for Hall to remember as he completed his hat-trick on 59 minutes when he received the ball just outside the box from Lewis Baker and he curled an effort past Cisak.
Jay Simpson did get the O’s on the scoresheet when he cut inside off the left and fired past Martin.
Lewis Baker struck the post with a 25-yard effort, before the hosts had penalty appeals turned away when Rob Hall went down in the box.
Simpson’s fierce cross forced a corner, but Alli rounded off the win with another curling effort from just inside the box.
And the hosts ended on top as Alex Cisak produced a fine stop to tip Lewis Baker's effort on to the bar and behind for a corner.
MK DONS: Martin, Lewington, McFadzean, Kay, Potter (Hitchcock 64’), Bowditch (C Baker 79’), Grigg (Cole 64’), Spence, Alli, L Baker, Hall.
SUBS: Burns (gk), Hodson, Green, Powell.
GOALS: Bowditch 22’, Hall 24’ 37’ 59’, Grigg 29’ pen, Alli 81’
ORIENT: Cisak, Cuthbert, Clarke (c), Baudry, Lowry, Taylor (Batt 46’), James, Bartley, McAnuff (Hedges 70’), Simpson, Dagnall (Plasmati 61’).
SUBS: Sargeant (gk), Omozusi, Mooney, Wright.
BOOKINGS: Baudry 86’ James
GOALS: Simpson 69’
ATTENDANCE: 10,137 (905 Orient fans)