Hannah Turtle, 22, denies murder, three charges of ill-treatment and two of administering poison.
But a court heard that she put her own anti-depressant drug in James’ milk bottle and stopped him breathing on three occasions over a 10 day period- the last of which resulted in his death, Wales Online reports.
Ms Turtle admits all the incidents but denies murder and says she did not intend to kill her son or to cause him really serious harm.
The trial of the mum from Shotton, North Wales, started at Mold Crown Court this morning and is due to last up to three weeks.
Prosecuting barrister David Elias, QC, said Turtle was careful that no-one witnessed her attempts to suffocate her son.
“We may never know why exactly she did this,” said Mr Elias.
“The prosecution say that she knew what she was doing and she knew the serious harm she was causing her young son.”
He said that on May 31, 2016, she deliberately pinched his nose so that he was unable to breathe and he turned blue.
Paramedics were called, he received hospital treatment and he was discharged back to his family, apparently in good health.
But the following day, on June 3, when alone with her son, she allegedly deliberately suffocated him again when he became floppy.
He was resuscitated, he suffered a fit on the way to hospital, and doctors could find no medical reason for his condition.
James returned home on June 6 but three days later the prosecution say she murdered him.
Mr Elias said that she put her hand over nose and mouth and stopped him breathing despite the fact that he was struggling against her.
He was flailing his arms about and it went on for between five to ten minutes, he said.
She allegedly sat with his life-less body for several minutes, went to check on her mother in law, went to the toilet and on her return to her room, pretended that she had just found him.
Unfortunately James did not recover from the last episode, he suffered brain damage from a devastating lack of oxygen and blood, and died in hospital on June 13 at 58 days old, Wales Online reports.
“The prosecution say that he was killed by his mother,” the prosecutor said.
Turtle initially denied being responsible but then told a social worker and repeated it to a nurse that she had killed him.
She said she needed help and had heard voices telling her that she did not deserve James.
“I wish I had never done it.
“I know I need help,” she said.
The jury was told that when refused permission to go to the funeral she made false allegations against her partner Ian Hughes.
But in a later letter to the police she admitted that she was responsible.
The jury was told that it could hear evidence about her psychiatric condition.
The child was taken to hospital from the family home in Shotton, on 9 June 2016. He died on 13 June.
He was initially treated at the Countess of Chester Hospital and was then transferred to Liverpool’s Alder Hey Children's Hospital where he died.
The trial is expected to last up to three weeks .