The A3 Northbound by Ripley Bypass in Surrey has been shut off for over nine hours following the incident at around 1.40am.
Police were called to reports of two loose horses being hit by a lorry on the A3.
Shortly after, a separate call came in about a crash with a car and another horse.
A Surrey Police spokesperson said: “Sadly, three horses were found deceased at the scene upon officer arrival.
“Officers are engaging with the drivers of both vehicles as part of ongoing enquiries.
“The road has temporarily been closed and diversions in place as Highways England look to carefully remove the deceased horses from the main road.”
The road remains closed from A247 in Burntcommon to Ockham Road North.
There is also congestion to Stoke Crossroads back into Guildford.
Highways England is now managing the road diversions with Surrey Police no longer involved.
At the time of publication, there is no indication on when this will reopen.
