Bidhya Sagar Das, 33, was arrested on Sunday after Scotland Yard launched a manhunt for him on finding the two children in a critical condition in a flat in Hackney area of north-east London.
The boy, named locally as Gabriel, died in the early hours of Sunday and the girl, Maria, continues to fight for her life in hospital.
Das is expected to appear before Thames Magistrates' Court in London later today.
The Metropolitan Police said detectives from the Homicide and Major Crime Command, led by Detective Chief Inspector Dave Whellams, continue to investigate.
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"This is clearly a tragic incident, and our thoughts are with the family of the two young children,"Whellams said.
According to local reports,the twins lived on the top floor of the building on Wilberforce Road near Finsbury Park in London with their Romanian mother, Cristinela Datcu, and Indian-origin father.
Horrified neighbours had reported a woman, believed to be the children's mother, rushing out of the home screaming, "My kids, my kids!" shortly after 11pm on Saturday.
It is believed the mother was locked in the bathroom as the children were attacked with a hammer.
Das worked as a hotel receptionist nearby but quit his job recently.
He lived with his Romanian girlfriend at the flat, which is now a crime scene.