Mikhail Clodt was born to the artistic family of barons Clodt von Jürgensburg, his father Konstantin Clodt was the first Russian wood engraver, his uncle Peter Clodt von Jürgensburg was a famous Russian sculptor.
He learnt drawing at the Saint Petersburg Mining Cadet Corps, then at the Imperial Academy of Arts (1851–1858). After receiving a Large Gold Medal he received a scholarship for three years to study painting in France, Switzerland and Italy but abandoned his foreign trip in a year. He complained that the foreign landscapes would not inspire him and that French and Italian school of painting is inferior to Russian one. After returning Clodt got permissions to use the rest of the scholarship funds in his travel over Russia.