Born in Helmstedt, his father, Johann Ernst Schubert, was a professor of theology and abbot of Michaelstein Abbey.
Since the major was fond of mathematics and astronomy, Theodor had to study these himself to be able to teach those subjects.
He moved on to Haapsalu, teaching mathematics to young noblemen as a preparation for a life as an officer.
He also wrote for the newspapers and for the German language St. Petersburger Zeitung, which he edited from 1810 until his death.
His son Friedrich von Schubert was a general in the Russian army and explorer.