It will contain a video of Ms O'Brien's funeral, which they missed while in Starship hospital, the funeral order of service, newspaper clippings about the accident and other items.
"When they start asking more detailed questions when they get older, I'll be able to sit them down but the memory box will be there until then."
Ms O'Brien's jewellery and other photos and keepsakes would also be kept for the children.
On Friday the pair were discharged from Tauranga Hospital and now live with Mr Ruddell and his parents.
Phoenix sleeps on a hospital bed in the lounge and is unable to travel in a car because of the casts which cover him from chest to toe.
He cannot go to the toilet unaided and can only leave the house in a wheelchair or ambulance.
The three adults take turns sleeping in the lounge with Phoenix in case he needs anything during the night.
Mr Ruddell said his son, who will be 5 in August, must learn to walk again when the casts come off and may miss his first weeks at school.
But he said the previously "full-throttle" boy, who was into trampolining and riding a balance bike before the crash, is coping well.
On Saturday "he was quite content" to build Lego with a friend who came to visit.
Faith, who is more mobile with just one leg in a cast, has mastered the stairs in the two-storey home and, despite getting tired faster because of her head injury, is back to her quirky self, "causing mischief", he said.
Mr Ruddell and Ms O'Brien were together more than six years before splitting up and remained in contact through shared custody.
"I still think the whole thing is surreal, like I'll wake up tomorrow and the whole thing will have been a dream. But I want to remain strong for the kids," he said.
A Givealittle fundraising page has raised nearly $11,000.
Horror journey
May 3: Tracey O'Brien's car veers into the path of another at Te Puna north of Tauranga. She is killed and her children, Phoenix and Faith, are seriously injured. The children are taken to Tauranga Hospital and flown to Starship in Auckland.
May 4: Phoenix is in an induced coma in the paediatric intensive care unit where both his legs are re-set and Faith is released to a ward from the HDU.
May 12: The children miss their mother's funeral at Omokoroa Community Church.
May 19: Phoenix and Faith travel by ambulance to Tauranga Hospital where they are admitted.
May 25: The preschoolers are discharged home to the care of their father and grandparents.