The incident allegedly happened at the Broadway Mall in Hicksville.
Police say a passerby discovered the two children unattended in a Dodge Neon in the Macy's parking lot at the mall around 9:40 p.m. Wednesday.
The boy and baby girl had apparently been left alone for at least 25 minutes in 28 degree weather.
The mother, 28-year-old Tanasia Perry, was charged with two counts of endangering the welfare of a child.
Eyewitness News is told the children were placed in the custody of their father.