The present invention discloses a method of encapsulating a wafer level microdevice, which includes: fabricating a microdevice on top side of a first silicon wafer; depositing a first capping carbon film on the top side of the first silicon wafer; implementing a backside fabricating process of wafer from bottom side of the first silicon wafer by carrying the top side of the first silicon wafer through the first capping carbon film; removing the first capping carbon film by selective gaseous reaction with carbon; and encapsulating an encapsulation wafer onto the top side of the first silicon wafer. The present invention deposits and removes the first capping carbon film by means of chemical technology, thereby protecting the microdevice on the top side of the first wafer during implementing the backside fabricating process of wafer. The top side does not need to be protected through the encapsulation wafer before implementing the backside fabricating process of wafer, which makes the wafer thinner and convenient to be handled.