Objective To study the effects of five tuina manipulations in rats with deep vein thrombosis (DVT) and to explore how to safely perform tuina in the treatment of thrombotic diseases. Methods Seventy-two male Sprague-Dawley (SD) rats were randomly divided into the model, pointing manipulation, plucking manipulation, kneading manipulation, pushing manipulation, and pulling manipulation groups (n = 12). DVT model was established by incomplete ligation. The tuina intervention was started on the next day after modeling and applied once a day 10 times by the manipulation simulators. On the 3rd and 10th days after intervention, respectively, the effects of tuina on thrombosis were evaluated based on thrombus elasticity, blood coagulation, fibrinolytic function and blood rheology with the ultrasound elastography, four coagulation tests, enzyme linked immunosorbent assay (ELISA), and hemorheology tests. Results In the pointing manipulation group, the strain rate ratio, 6-ketoprostaglandin F1α (6-Keto-PGF1α), and high shear rate were decreased, and the thromboxane B2 (TXB2) content was increased (P < 0.05). In the plucking manipulation group, the D-dimer and 6-Keto-PGF1α contents were increased, prothrombin time (PT) was shortened, and activated partial thromboplastin time (APTT) was activated, and the high shear rate and plasma viscosity were decreased (P < 0.05). In the kneading manipulation group, APTT was shortened, and 6-Keto-PGF1α, high shear rate, and plasma viscosity were decreased (P < 0.05). In the pushing manipulation group, the strain rate ratio, low shear rate, and high shear rate were all decreased (P < 0.05). In the pulling manipulation group, both the strain rate ratio and the low shear rate were decreased (P < 0.05). The 6-Keto-PGF1α changes on the 3rd and 10th days after intervention were opposite in the pushing manipulation group and the pulling manipulation group (P < 0.05). Conclusion The pointing, pushing, and pulling manipulations seem to be safe in the early period of thrombosis, but the risk is likely to be elevated as the treatment course of intervention increases. The plucking and kneading manipulations potentially have certain risks in the treatment of DVT in rats.