Cox joined the club to replace Wayne Johnson back in October when the Blues were in serious danger at the wrong end of the table but, after bringing in a number of quality players, the former Premier League defender steered the club to safety with a couple of weeks to spare.
Citing ‘personal reasons’ for his departure Cox said, “I would just like to thank everybody at the club especially the Chairman and the Board of Directors.
“I’ve really had a great time here and the club has really looked after me so I’d like to thank them for that.
“Most of all I’d like to thank the fans – we’ve had some difficult times but they’ve always stuck by me especially all those travelling fans who give it their all week in week out”, he added.
Commenting on the manager’s decision, Club Chairman Andrew Wain said, “I was shocked to receive Neil’s resignation but I understand why he has decided to leave.
“First and foremost we’d like to thank him for having faith with some of our established players and the quality of those he brought in.
“Neil was a pleasure to work with and was in our bigger plans for the future.
“However, we wish him all the best and hope he will be back in the game somewhere in the not too distant future”, he added.
Cox’s record during his seven month tenure was: won 10; drew 3; lost 11. He also made one full appearance and three others from the bench after registering himself as a player.
Assistant manager Stuart Heeps will take charge of the two remaining games and the position of manager will be discussed at Board Room level at the end of the campaign.
Cox, 39, began his career as a defender with home town club Scunthorpe United in March 1990 where he remained for just twelve months before being snapped up by Aston Villa for £400,000.
A fee of £1M took him to Middlesbrough in July 1994 and Bolton paid a further £1.5M for him three years later.
In November 1999 he moved on to Watford in a £500,000 deal and became team captain before joining Cardiff City and then Crewe Alexandra in June 2006.
In a career spanning almost 20 years, Cox was capped at Under-21 level six times by England and made 617 senior appearances as a pro scoring 42 goals.
After retiring from the game in May 2008 he became a property developer in Portugal.