The health status of the honey bee Apis mellifera has been challenged globally by the ubiquitous ectoparasitic mite Varroa destructor over the past several decades. The resistance of the mite to and residue accumulation of the traditional acaricidal treatment call for more natural and safer alternatives to control this parasite in colonies. Essential oils originating from plant foliage are considered to be a potential substitute. In this study, we evaluated the fumigant activities of eleven essential oils derived from Chinese crude medicines. Appropriate dosages that did not severely harm honey bees were applied in a toxicity screening test of V. destructor mites. Six essential oils had significant acaricidal activities against the mites, and Odoriferous Rosewood oil and Fennel oil caused more than 65% V. destructor mortality. Meanwhile, the fumigant toxicity of all of the essential oils on adult honey bee workers was not significantly different from that of controls. We then measured the selectivity indexes of the six essential oils mentioned above by determining the LD50 values for honey bees and for V. destructor mites. Considering both the toxicity to the bees and to the mites, Odoriferous Rosewood oil and Fennel oil showed great potential for varroacidal application as a fumigant agent. This study identified new essential oils with acaricidal properties that might contribute to mitigating the poor health status of A. mellifera colonies due to V. destructor infestation.