Carroll suffered a fresh foot setback earlier this week as he was nearing recovery from an initial injury that kept him out of the Hammers' opening matches of the season.
The England international is likely to be sidelined for a substantial amount of time in World Cup year, and Allardyce believes that the psychological side of his recovery is just as important as the physical side.
"It is a big challenge for Andy because he has got to be mentally really tough now," Allardyce told PA.
"He has to be really, really focused and we have got to make sure we keep his spirits up whenever we get the chance because it is a lonely place to be when you are injured, and certainly for the length of time he has been injured.
"This will make him feel pretty low for a while, but he has to battle through that and we will look after the psychological side as well as the physical side. At the end of the day it is just about getting him fit as quick as we possibly can."
Carroll joined the Hammers from Liverpool for a fee of £15m this summer having spent last season on loan at Upton Park.