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Controlling fertility of rodent pests has become a widely used means of controlling populations of grassland rodents in China. Research has recently focused on environmentally-friendly fertility inhibitors that lead to a more sustainable control of pest rodent populations. Using plant-derived fertility inhibitors may be an appropriate method. In this study, we used experimental populations of wild mid-day gerbils (Meriones meridianus Pallas) the dominant rodents in typical Chinese desert regions to test the effects of shikonin-quinestrol (ND-1) (also known as Nong Da-1), a new plant-derived fertility inhibitor. Mid-day gerbils were divided into control, female treatment and male treatment groups, and the effects of the fertility inhibitor ND-1 were studied. We found that there was a significant decrease in average litter size in the male treatment group (P < 0.01) during the first breeding period of the gerbil’s annual breeding season. The average litter size of the male treatment group was 1.42 +/- 0.12 individuals and the fertility suppression rate was 42.86%. The second litter showed a significant decrease (P < 0.05) in the average litter size in both female and male treatment groups (1.42 +/- 0.13 and 0.14 +/- 0.04 individuals, respectively) and fertility suppression rates were 57.14% and 85.78%, respectively. The control group bred two to three times during the breeding season, while the two treatment groups bred zero to two times, which was significantly lower than the control group (P < 0.01). Reproductive start-up periods (RSP) of the two treatment groups were delayed. The female treatment group showed a 15-22d delay in reproductive period, and the male treatment group showed a 32-157d delay. The fertility inhibitor ND-1 induced infertility in both males and females. As a plant-based agent, ND-1 is an effective and non-polluting agent for inhibiting fertility in mid-day gerbils.