The firm hopes to start demolition work on April 24 and complete it by June 2.
A new one will then be built in its place, with a planned Easter 2018 opening.
It follows a huge fire that ripped through the service station in December 2016.
Fire crews from across Surrey and Hampshire rushed to the blaze on December 14 at around 10.30pm which left part of the service station in ruins.
It took firefighters until 2.30am the following morning to control the flames.
The M3 was closed in both directions overnight as smoke billowed across the road.
The following morning, eerie pictures of the devastation emerged showing the extent of the damage from the fire. No one was injured.
A large temporary building opened on March 23 and houses a Starbucks, a small Waitrose, Burger King, Harry Ramsdens, WH Smith, Chopstix and a Starbucks Drive Thru.
It will remain in place until the new building is up.
Welcome Break has submitted a construction management plan with its application to demolish the fire-damaged building.
Part of it states: “The current southbound services suffered an extensive fire in December 2016 and the building is now in need of demolition, which will form the first phase of the works on site, with further phases incorporating a new state of the art services to match the current requirements of a modern day motorway amenity building."
“Due to the close proximity of adjacent properties, noise and dust pollution from site works will be one of the most sensitive issues to the neighbours," according to the document.
“The volume and movement of traffic we envisage will not have any adverse impact on the neighbours, due to the current use of the area as a 24/7 amenity building.”
The construction management plan also states that all personnel on site will undergo environmental training, all relevant plant will comply with permissible noise levels set out in European directives, and where possible plant will be fitted with reversing alarms.
Vibration monitoring will be undertaken as required and a site speed limit of 10mph will be in force.
No delivery vehicles will be allowed before 8am or after 3.30pm on weekdays and deliveries will not be accepted at weekends unless otherwise agreed.
Hartley Wintney Parish Council has already decided to raise no objection to the application.
Hart District Council is still considering the application.