Australia's Lyon determined to bounce back after surgery
The 38-year-old faces an extended period on the sidelines after damaging his right hamstring saving a boundary on day five of the third Ashes Test in Adelaide.
McDonald said Lyon remained a key part of their plans as reports speculated that his 141-Test career could be over.
It is the second serious injury Lyon has sustained in two years after being ruled out of the previous Ashes series against England with a calf injury picked up at Lord's in 2023.
He had surgery on Tuesday, but was expected to be with the team during the fourth Ashes Test in Melbourne starting Friday.
"He's pretty shattered," McDonald told cricket.com.au late Tuesday. "He's a huge part of what we do.
"He's facing a long recovery timeframe. That type of injury, it's going to be a hard period for him to get back to where he was.
"But he still wants to do it and that's the main thing."
After the final two Ashes Tests in Melbourne and Sydney, Australia's next series is not until the middle of 2026, when they host Bangladesh.
After that is a busy period culminating in a five-Test tour of India from late-January 2027, and then the 150th anniversary Test against England in March.
"India's on the horizon, he'll be a key part of that," McDonald said of Lyon.
"We've got New Zealand (and) South Africa before that. So, get through this rehab and then (we'll) look forward."