The 25-year-old Russian skier covered the 15 km distance in 32 minutes 29.8 seconds.
Bolshunov lost 3.4 seconds to the winners of the race to the Norwegian Johannes Klebo.
The bronze medal was won by Sjur Röthe (4.0) from Norway.
Earlier, Klebo reacted to the silver medal of the Russian Bolshunov in the classic 15 km time trial at the first stage of the Tour de Ski in Lenzerheide, Switzerland.