Variations on the efficacy of commercial Ginkgo biloba preparations have been reported, although all the products follow the same standards. Terpene trilactones (TTLs), including bilobalide (BB) and ginkgolides, are one of the main active components in G. biloba extract and have been received the most attention due to their chemical uniqueness and their importance for quality control. A plenty of studies demonstrated that BB and ginkgolides display differential activities on various biological processes. However, the influence of different ratios of BB and ginkgolides on the efficacy of TTLs has not been detected yet. The aims of this study were: (1) to test whether different ratios of BB and ginkgolides existed in commercial G. biloba preparations; (2) to detect the influence of different ratios of BB and ginkgolides on the in vivo efficacy of TTLs; and (3) to optimize the extraction process of G. biloba to approach the better BB and ginkgolides ratio with the maximum in vivo effects. First, the content and proportion of BB and ginkgolides in various G. biloba preparations were quantified by HPLC-MS analysis. As the results, an obvious fluctuation in the proportion of BB and ginkgolides was observed in the preparations from different commercial suppliers. The ratio was ranged from 0.3 to 0.8. Second, a zebrafish thrombosis model was used to evaluate the antithrombotic effects of different ratios of BB and ginkgolides. The result showed that the proportion of BB and ginkgolides at 1:2 produced the maximum antithrombotic effects. Third, the extraction process of G. biloba was optimized using a design space technique aiming to approach the best BB and ginkgolides ratio obtained from zebrafish experiment. The extraction process was modeled based on the results of Box-Behnken designed experiments. Design space was then calculated using a probability-based method. Within this design space, G. biloba extraction process can be guaranteed to achieve the better BB and ginkgolides ratio with high assurance. Normal operation space for G. biloba extraction process was recommended as ethanol concentration of 50% to 70%, liquid-to-solid ratio of 5.6 mL/g to 7.3 mL/g, and extraction time of 2.2 h to 3.0 h. This work not only suggest that the proportion of BB and ginkgolides should be used as a quality control index in ginkgo preparations besides the content of TTLs, but also provide a way to approach it with the extraction process parameters controlled in the normal operation ranges.