Anias, who was already struggling before the operation, is having more difficulties, regularly contracting viruses and infections.
But their surgeon Dr Philip Goodrich said he believes Anias will pull through, and he thinks Jadon is a great force of energy for him at this time.
"Separating the two is probably not a good idea at this point," he told CNN.
The boys were born via cesarean section last September near Chicago, Illinois. They were attached by the crown of the head.
Nicole and 37-year-old Christian insisted the boys were perfect as they were.
But in order to let them lead a normal life, they traveled to Montefiore Hospital in the Bronx, New York, to have one of the world's most esteemed surgeons perform the incredibly rare operation to separate their heads.
The operation costs $2.5million.
"This is so hard. I'm not going to sugarcoat it," Nicole said before the operation.
Anias and Jadon, who have a three-year-old brother Aza, were technically called "craniopagus twins" - a phenomenon that occurs just once in every 2.5million births.
Based on national statistics, it is astonishing they made it to 13 months.
After the procedure, he continued to have seizures but doctors put him on medication that stopped those attacks last month.
She did, however, get to hold Jadon, and described the moment in an emotional post on Facebook.
She said it was always her goal to be able to rock her 13-month-old son Jadon - something she could not do when her sons were conjoined at the head.
"For over 13 months, I've dreamed of this moment," Mrs McDonald wrote.
"I looked down at Jadon's angelic face and saw him in a way I'd never seen him before.
"He whimpered for almost the whole two hours I held him because he had just been extubated, had the area under his scalp washed out and had been weaned from the good pain meds.
"But instead of wrapping my body around him in his bed, I wrapped my arms around him and rocked. One of the most profound moments of my life."
The operation was performed by Goodrich, a neurosurgeon who specializes in separating conjoined twins at the head.
Dr Oren Tepper, a plastic surgeon, was in the room to reconstruct the skulls and stitch each head closed.
The team has spent months practicing and planning their strategy using a physical 3D model of the boys' heads, plus computerized 3D modeling, where they can look at different scenarios.
A Go Fund Me page was made to help the family with the cost of the expensive surgery.