Walcott, who injured his shoulder in the 5-2 victory over Tottenham, will be joined in the stands by Andre Santos.
However, left-back Kieran Gibbs and Ivory Coast forward Gervinho return from injury to make the Gunners squad.
Benjamin Stambouli (virus), injured forward John Utaka, full-back Garry Bocaly and suspended striker Souleymane Camara are all out for Montpellier.
"The injury he got during the game with his shoulder, we have to scan that and see if there is no damage," said Arsenal boss Arsene Wenger of Walcott's injury. "It should be short-term.
"We will miss Andre Santos as well, who has a muscle strain in his abdomen."
Arsenal are second in Group B with two games remaining and know they will qualify for the knockout stages if they beat Montpellier and Olympiakos lose to Schalke 04.
Schalke, who lead Arsenal by one point, will confirm their own progression if they defeat Olympiakos on Wednesday.
If the Greek side avoid defeat in Germany, they will take qualification down to the final game when they host Arsenal on 4 December.
Likey Line-ups:
Arsenal
Montpellier
Source: DSG
Source: DSG