A method of manufacturing a micro structure, includes the steps of: preparing separate first and second substrates, the first substrate having a first surface on which a first structural body having a first height and a second structural body having a second height greater than the first height of the first structural body are arranged, the second substrate having a second surface; then placing the first and second substrates to cause the first and second surfaces to face each other across the first and second structural bodies; and then bonding the first and second substrates to each other while compressing the second structural body in a height direction thereof between the first and second surfaces to cause the second structural body to have a height defined by the first structural body.