This work aims to explore the feasibility of using type D botulinum toxin as a novel, environmentally friendly biological rodenticide for the population control of rodents in plateau pastoral area. The toxin is subjected to toxin component, DNA sequencing, and bioinformatic analyses. The lethal median dose (LD50) values of intragastrically and orally administred type D botulinum toxin in wild plateau pikas, plateau zokors, and Microtus fuscus are calculated through Horn’s method and the improved Karber method. The ability of the toxin to prevent and control rodent damage is assessed through plot experiments. The safety of type D botulinum toxin toward nontarget animals, such as yaks, Tibetan sheep, dogs, vultures, and birds, is also tested. Results show that the toxin is encoded by a type D botulinum neurotoxin gene. The DNA and amino acid sequences of the full neurotoxin gene comprise 3831 base pairs and 1276 amino acid residues, respectively. The nucleic acid and protein sequences of the toxin exhibits 99% homology with those of a known type D botulinum neurotoxin gene, and the composition of the functional domain of the toxin is consistent with that of type D botulinum neurotoxin. For plateau pikas and plateau zokors, the LD50 values of intragastrically administered type D botulinum toxin is 6810 and 5840 MLD/kg weight, respectively, and those of orally administered type D botulinum are 1.231and 1.319 g/kg weight, respectively. The natural enemies of rodents are strongly resistant to type D botulinum toxin. Experimental results indicate that type D botulinum toxin can be used as a new biological rodenticide for the prevention and control of rodent damage in plateau pastoral area.