Purpose: To compare the effects of FK-506, cyclosporin A (CsA), and sodium hyaluronate (HA) eye drops for the treatment of botulinum toxin B (BTX-B)-induced mouse dry eye. Methods: CBA/J mice were randomized into 5 groups. The groups received treatment with eye drops containing 0.025% FK-506 combined with 0.3% HA (FK-506+HA group), 0.025% FK-506 (FK-506 group), 0.05% CsA (CsA group), 0.3% HA (HA group), or 0.9% saline (saline group) 3 days after an intralacrimal gland injection with 20 mU of BTX-B. Tear production, corneal fluorescein staining, blink rate, and the mRNA and protein expression levels of inflammatory cytokines were measured. Results: FK-506+HA eye drops increased tear production and reduced the corneal fluorescein staining scores at all time points after treatment compared with those in the saline group. Compared with those in the saline group, the tear production and severity of corneal epithelial defects in the FK-506 group were significantly improved at weeks 2 and 4. Compared with the saline eye drops, the CsA eye drops ameliorated only tear production and corneal fluorescein staining scores at week 4 after administration. The FK-506+HA, FK-506, and CsA eye drops downregulated the expression of inflammatory cytokines in both the keratoconjunctival tissues and lacrimal glands at week 4. Conclusions: The topical application of 0.025% FK-506 combined with 0.3% HA, 0.025% FK-506, or 0.05% CsA can suppress the expression of inflammatory cytokines and can alleviate the signs of dry eye. Topical application of 0.025% FK-506 combined with 0.3% HA showed the best therapeutic effect and may be a possible therapy for dry eye.