The proposal is for 20 minutes free parking in the town centre but business owners are annoyed longer term free spaces will become pay and display bays, if plans go ahead.
They also say they are being encouraged to pay hundreds of pounds for business permits to park on their doorsteps - a fee many claim they cannot afford.
Julie Donabie of My Favourite Things, Worple Road, said: "People park here because they have businesses here and there is no car park.
"Businesses will close because they can't survive and visitors won't come because they can't park."
Osteopath David Rowland of the Wimbledon Osteopathic Clinic in Worple Road said it is the permit that would affect his business the most.
He said: "Small businesses are what keep this country going.
"The council want to hinder small businesses as much as they can.
"We will have no choice but to apply for the permit, but we will fight it."
Councillor Andrew Judge, cabinet member environmental sustainability and regeneration, said the proposals were partly designed to discourage commuters from parking in residential roads.
Coun Judge said: "We are concerned across the borough to improve parking for businesses and that has to be balanced with parking for residents.
"Sometimes people have misplaced concerns and they believe it will be a damaging affect when the opposite is the case."
He added businesses are entitled to apply for permits and the tariff is the same across the borough.
The proposed changes include pay and display bays to be installed in Durham Road.
Currently there are free spaces from 10am to 4pm with a maximum stay of one hour, but this will be converted to paid for spaces with a maximum stay of two hours.
Opposite Sainsbury's Local in Worple Road, it is proposed to convert the existing free spots to pay and display with a maximum stay of two hours.
A consultation on the changes and ends Friday, February 7.
To comment on the plans, write to the head of street scene and waste, Merton Civic Centre, London Road, Morden, SM4 5DX or email firstname.lastname@example.org quoting reference ES/SGE/RPTC.
- Update: Man dies after collapsing at gym in Wimbledon - Nuffield Health Centre to remain 'temporarily closed'
- Whose land is it anyway? Anger over 'filthy' fly tipping in conservation area that no one takes responsibility for
- WATCH: Moment Merton Council enforcement officer is violently kicked off Morden bus
- FEATURE: Is enough being done to tackle air pollution?
- 'It's like she's transported to another world': Care home residents shown biographical films in clinical trial