This study generated two fused protoplasts of Antrodia cinnamomea and Cordyceps militaris in two ways. The protoplasts of A. cinnamomea were inactivated by heat to inactivate biochemical processes and enzymatic activities in the cytoplasm, and the protoplasts of C. militaris were inactivated by UV radiation to invalidate their genome function, then they were fused under optimal conditions to get a fusion rate as (7.42 ± 0.8) × 10^-6 fusants/mL; the new fusants were abbreviated as Ac-Cm. On the other hand, when A. cinnamomea and C. militaris were treated with heat and UV oppositely using similar experiments, the fusion rate was (9.70 ± 0.68) × 10^-5 fusants/mL, and the new fusants were abbreviated as Cm-Ac. We selected each of two best-growing fused colonies Ac-Cm-1, Ac-Cm-2, Cm-Ac-1, and Cm-Ac-2, together with parental A. cinnamomea and C. militaris, and studied their morphology, growth antagonism tests, and genetic relationships by 18S rRNA sequencing. In comparison with the initial cultures of 4 fusants, the yields of adenosine, biomass, cordycepic acid, cordycepin, total polysaccharide, and total triterpenoids were increased up 1.305−50.1563 times in the optimal medium conditions. For gene stability tests, those of the four fusants and their outputs were stabilized within 10 generations.