Objective To investigate the pharmacokinetic behavior and in situ intestinal absorption of evodiamine complex water-in-oil nanoemulation (WECNE). Methods WECNE was formulated with the titration stirring methods. Twelve male SD rats were intragastrically administered with evodiamine (EDA) and WECNE at the same EDA dose of 100 mg·kg^-1. Blood samples were collected from eye socket at 0.083, 0.25, 0.5, 0.75, 1, 2, 5, 8, 12, 24, 48 and 72 h after intragastrical administration, and the plasma concentrations of EDA were determined by RP-HPLC. DAS 2.1.1 software was applied to evaluate the pharmacokinetic behavior. Single-pass intestinal perfusion was carried out to test the intestinal absorption in situ. Results The area under the curve (AUC_{0-72 h}), peak concentration (C_max) and time to peak (T_max) of WECNE were (4 924.59±1 105.28) μg·L·h^-1, (305.47±51.23) μg·L^-1 and (0.83±0.29) h, respectively. The absorption rate constant (Ka) of WECNE in the stomach, duodenum, jejunum, ileum and colon were (1.05±0.82)×10^-5, (12.19±1.57)×10^-5, (12.66±1.35)×10^-5, (11.94±4.17)×10^-5 and (11.21±1.25)×10^-5 L·s^-1, respectively. In addition, the effective permeability (P_eff) of WECNE in the duodenum, jejunum, ileum and colon were (26.03±3.84)×10^-5, (18.48±5.99)×10^-5, (19.77±2.59)×10^-5 and (36.02±1.48)×10^-5 cm·s^-1, respectively. Conclusion WECNE can improve the bioavailability and the absorption in situ of EDA in different parts of the gastrointestinal tract.