The blackberry seed was typically removed as a byproduct and waste from blackberry fruits for juices. Developing value-added utilization of berry seeds will significantly expand the market for berry products as well as improve benefit to berry producers. However, the research on blackberry seed is limited. The objective of this paper was to research antithrombotic mechanism of polysaccharides in blackberry seeds. Polysaccharides in blackberry seeds were extracted, purified and identified by high-performance gel permeation chromatography (HPSEC), gas chromatography (GC), fourier transform infrared (FT-IR) spectrometer and nuclear magnetic resonance spectra (NMR). Anticoagulant activities were evaluated in vivo by measuring activated partial thromboplastin time (APTT), thrombin time (TT), prothrombin time (PT), fibrinogen (FIB) and plasma recalcification time (RRT). Four polysaccharides named BSP-1a, BSP-1b, BSP-2 and BSP-3 were isolated from Blackberry (Rubus spp.) seeds. The results indicated that BSP-1b, BSP-2 and BSP-3 exhibited the anticoagulant activity. Therefore, the anti-thrombosis effects of BSP-1b, BSP-2 and BSP-3 were investigated in vivo by 6-Keto-PGF1α, thromboxane B2 (TXB2), endothelial nitric oxide synthase (eNOS), endothelin-1 (ET-1), whole blood viscosity (WBV), plasma viscosity (PV), hematocrit (Hct), erythrocyte sedimentation rate (ESR), APTT, TT, PT and FIB. The results suggested that BSP-1b, BSP-2 and BSP-3 had the inhibition effect on thrombus formation, and the antithrombotic effects were associated with the regulation of vascular endothelium active substance, activating blood flow and anticoagulation effect.