World Vision believes the harsher conditions will claim the lives of many desperate people who still have no option but to flee their home country.
It is calling on EU nations to do more to help.
Brenda Yu, spokesperson for World Vision UK, told Premier: "Winter is coming and unless we start scaling up our operations these refugee families won't be able to survive.
"We need to see more shelters, more blankets, more winter clothing and water. EU leaders need to fulfil their legal and moral obligations to protect these refugees who are coming to Europe."
Around 8,000 people a day have been crossing the borders into Europe since the current crisis began and the UN estimates a figure close to this will continue for some time.
Ms Yu said: "When I was at the border crossing between Serbia and Croatia I saw families lying lifelessly on the ground with nothing but their thin winter jackets.
"I spoke to a mum who tearfully told me that her eight year old girl, after being on a boat to Greece for twelve hours, said to her 'mum I just want to die'.
"The temperature was minus three degrees. It will continue to drop but that won't stop refugee families from crossing into European countries. They don't have a choice."
On Wednesday EU leaders met counterparts from Africa at a summit in Malta.
The European Commission says it will give €1.8bn (£1.3bn) to African countries in exchange for help with the migrant crisis and it expects EU nations to pledge more.
The aim is to tackle the economic and security problems that cause people to flee, and persuade African countries to take back more failed asylum seekers.
Ms Yu added: "Urgent action is needed otherwise we will see a whole new scale of the humanitarian crisis in Europe.
"Funding is incredibly short and we need EU leaders to commit more. This could be the last chance."