Bogut says it will hurt not having NBA All-Star Simmons for the global showpiece tournament in China in September and it means the team will also play a different style of basketball.
Prior to that Australia play four warm up games in August - two against Canada in Perth and two against the US in Melbourne.
Simmons, who initially committed to both the lead up games and World Cup, last week withdrew from the latter after signing a $A242m, five-year maximum extension with the Philadelphia 76ers.
"He's the best Australian player in the world, so whenever you lose a guy that can go out there and give you 20 (points) 10 (rebounds) and eight (assists) on any given night, it's going to hurt," Bogut said on Monday.
"It will be interesting to see how that all plays out, because with Ben in the line-up we're playing a different style of basketball..
"It's going to be a tough one for the coaches to figure out - whether he plays big minutes in these lead-up games or he just he comes along and plays a bit more restricted, so we can at least get our flow going for the most important games at the World Cup.
"The Australian public want to see him play on home soil and we haven't had that for a long long time but it is a bit of a conundrum.
"There's no right or wrong answer to it and I guess the playing group and the coaches in camp will figure all that out on the fly."
Bogut warned the US, with five-time NBA title-winning coach Gregg Popovich at the helm, would still be the team to beat at the World Cup despite Simmons' 76ers teammate Tobias Harris becoming the sixth player to pull out of their squad.
"People are maybe pushing back towards (world governing body) FIBA and not really too excited to go to this thing, but we are," Bogut said.
"If we can get there and try to win a medal that's a goal for us and obviously this is just as importantly a qualifying tournament now for the Olympics, so we basically need to finish higher than New Zealand to get an easier route to the Olympics."