The decision was taken by the club and Scottish Rugby following a meeting with Wilson earlier today (Monday 6 June).
Scottish Rugby thanked Danny for his contribution over the past four years, firstly with the men's national team and subsequently with Glasgow Warriors.
The squad will break for the close season at the end of this week and the club will now begin a recruitment process for a new Head Coach.
Glasgow Warriors Managing Director, Al Kellock said: "The recent run of results has not been acceptable and has had a significant impact on everyone connected to the club.
"We are a proud organisation and want to be competitive week in, week out and we felt therefore a change of Head Coach was the right step to take.
"It is never pleasant to have to make changes to our team, but we needed to act. I've enjoyed working closely with Danny and know he has given a huge amount to Glasgow over the past two seasons and for that I'd like to thank him and wish him well.
Danny Wilson said: '"I am proud that we finished the season in the top eight and qualified for a quarter-final, and like everyone I am extremely disappointed with the result at the weekend.
"I'd like to thank the players and staff at Glasgow Warriors for all their hard work and commitment over the two seasons I was with the club."
Scottish Rugby Chief Executive, Mark Dodson said: "I'd like to thank Danny for his contribution to rugby in Scotland over the past four years.
"He faced a challenging period taking on the Glasgow role mid-pandemic and while there have been several high points, ultimately recent results have not been consistent enough and given the importance of our two professional teams we needed to address that in a timely manner.
"I have a lot of respect for Danny and the professional way he conducts himself and wish him well in the future."