While temperatures will continue to soar on Wednesday some areas will be lashed by heavy rain, hail and thunderstorms.
The forecaster said there was a risk of homes and businesses being flooded quickly as well as lightning strikes and hail to batter the area.
There is also a risk of power cuts as well as difficult driving conditions and road closures.
Two warnings have been issued, one for Wednesday from 11am until 9pm covering most of south west England and the south coast of Wales.
Another warning on Thursday covers Northern Ireland, Wales and most of northern and central England between 11am and 8pm.
The Met Office said many areas will avoid the worst of the showers, but “thundery downpours” could bring 30mm and 50mm of rainfall in less than three hours in some places.
Deputy chief meteorologist Dan Harris said: “The hot and clear weather currently being experienced across large parts of the UK is forecast to break down through the middle of the week as showers and thunderstorms arrive.
“These will initially affect the southwest of the UK on Wednesday, before moving steadily north and developing across most areas through Thursday and Friday.”
The mercury, which has soared in recent days, will stay hot reaching highs close to 30C, with much of the country set to bake.
It comes after the UK recorded its highest temperature since the end of July with the country baking in early autumn sunshine.
The mercury reached 30.7C at Gogerddan, in Dyfed, Wales, on Tuesday, the Met Office said.
It is the highest temperature since the 31.2 C recorded at the same location on July 22 this year.
Elsewhere, temperatures reached 30.4C at Northolt in west London, 30.3C at Pershore in Worcestershire and 30.2C at Heathrow, west London, and at Santon Downham in Suffolk.
The Met Office said that the recordings meant it was only the seventh time temperatures have exceeded 30C in September in the last 50 years.
Meteorologist Marco Petagna said the hot weather was “not that unusual” for the first half of September, but it would be “more unusual” for it to occur later in the month.
He said if a temperature of more than 28.1C was recorded in Scotland on Wednesday, it would be Scotland’s hottest September day since 1906.
UK Weather Forecast
Hot sunshine for many, although the far north and west of Scotland will be cloudier with some rain or drizzle at times. Showery rain, sometimes heavy with thunder, will affect parts of southwest England and south Wales, moving north later.
Clear spells across northern England and much of Scotland, whilst rain affects the far northwest. Showery rain moving north across other parts of England and Wales, some heavy with thunder.
Heavy, thundery downpours breaking out across parts of England, Wales and Northern Ireland, whilst more persistent rain affects northern and western Scotland. Some bright spells in between. Warm and humid.