Objective To evaluate the effect of desensitization therapy for the dust mites allergic conjunctivitis. Methods From 2002 to 2007, prospective and case controlled trial was designed to compare the scores of ocular itch and ocular hyperemia, levels of serum specific IgE and EOS before and after desensitization therapy of the 122 dust mites allergic conjunctivitis. Results There were 122 patients completed the therapy and in compliance with the evaluations. The scores of ocular itch decreased from (2.2± 1.1) before therapy to (0.5± 0.3) after therapy (P <0.01), ocular hyperemia decreased from (1.8± 0.9) before therapy to (0.4± 0.3) after therapy (P <0.01); levels of serum specific IgE of dust mites and EOS decreased from (41.01±6.96) KUA/L, (0.698± 0.378)× 109/L to (32.06± 2.98) KUA/L(P>0.05), (0.119± 0.127) × 109/L(P<0.01) respectively before and after therapy. 64.75% of the patients were clinically cured, 31.97% of them were clinically effective. There were 8 out of 122 patients appeared local side effects, and there were 2 out of 122 patients appeared systemic symptoms. Conclusion Dust mites specific desensitization therapy is an effective method for the dust allergic conjunctivitis.