Shelter management has faced pressure from trade union Unite since January over changes to staff contracts that will involve longer working hours and an end to incremental pay increases.
"I cannot emphasise enough how much this dispute has the potential to damage the reputation and standing of Shelter," writes McDonnell.
In a separate letter to Shelter's board, 10 MPs, including McDonnell and George Galloway, have said they disagree with Shelter's decision to dismiss staff who have refused to agree to reworked contracts.
The developments come in the wake of an early day motion, put down by McDonnell in February, that expressed regret at the actions of Shelter management and asked trustees to work cooperatively with the union. The motion received 45 signatures.
Last month, union members at the charity voted to refuse the management's offer of £150 compensation plus a non-consolidated payment equivalent to 2008 increments. They have held four days of strikes in the past two weeks.
A Shelter spokesman said: "Management have made a full and final offer to the union. We would ask the union to consider its position and end industrial action."