Kit Malthouse announced he had left his position at the MS Society after its members said they wanted him to go.
The charity said his support for cutting Employment Support Allowance (ESA) by £30 a week "prevented him from being an effective patron".
Mr Malthouse said there was a "wide misunderstanding" about the cuts.
The North West Hampshire MP voted to cut ESA, which replaced Incapacity Benefit, on 2 March.
After the Commons vote, the MS Society asked Mr Malthouse to resign.
The cuts will see new applicants' payments reduced from £103 to £73 a week - the equivalent of Job Seekers Allowance - from 2017.
In response, Mr Malthouse said: "I was sorry to hear that Andover MS Society do not want me to continue as patron... not least since MS has affected my wider family in the past."
The Tory backbencher said in a statement that current ESA claimants would not be affected by the changes and that keeping disabled people in work for as long as possible "is surely the best therapy of all".
The Work and Welfare Reform Bill passed through the House of Lords on 8 March.
Previously, the Lords had rejected the bill twice but government ministers invoked special budgetary powers to push it through the Upper House.
Speaking in the Lords, Paralympic Gold Medallist Baroness Grey-Thompson said cutting ESA would have a "dreadful and punitive" affect on disabled people.
The government has said that that although cutting the lower benefit rate would save £55m in the first year, £60m would be spent to help claimants find work.
A Conservative MP has been forced to resign as a multiple sclerosis charity patron after he voted in support of disability benefit cuts.