Quinestrol is a synthetic steroidal estrogen-type rodent infertility agent. Studies have shown that Quinestrol had an efficient sterile control effect on the reproduction of some pest rodent populations. The aim of this study is to test effects of Quinestrol application on the nesting behavior of Meriones unguiculatus population in the agro-pastoral transition zone in the Inner Mongolia. The rodent population controlling experiment was conducted on May, 2006, at the gerbil populations distributed in the agro-pastoral transition zone of Xilinhot City, Xilingol League, Inner Mongolia autonomous region. We settled two testing groups: the drug-administrated area and the controlled group of gerbils. In May, July, and September, 24 gerbil herds were randomly chosen and used the rodent hole counting method to investigate the herd size of the Mongolian gerbils both in the controlled area and the drug-administrated area. The variety of the density of gerbil holes and the effect of sterilization agent on the population size of the gerbils were calculated pre and post antifertility drug was applied. At the same time, the active ranges of 30 gerbil herds were randomly selected and measured both in the controlled group and the drug-administrated group, and the effect of quinestrol on the agro-pastoral zone was compared between pre and post stage of quinestrol usage. The results of quinestrol application were significantly reduced the size of all 54 gerbil herds. More narrowly, the population of the controlled area had an average of 58 burrows were observed, and there were only 23 burrows were found in the dosage area. The Mongolian gerbil population was controlled in the quinestrol dosage area that Mongolian gerbil population density in the drug-administered area continued to decline after drug administered, and the largest decline was 70%, which was lower than the population density in the controlled area. Investigation results of nest radius and active area of gerbils showed that: there were significant reduction happened after the administration of quinestrol, and the radius and activity reduction of dosage area was 15% and 30% lower than the average radius and the nest active area in controlled zone. Therefore, the application of Quinestrol had significant effects on controlling the wild gerbil population and reducing the home-range radius and activity area of the gerbils. The effects of single usage of quinestrol were meaningful for the prevention and controlling of rodent pests in agro-pastoral ecotone, as well as for the reduction of rodent-borne diseases, including the spread of plague.