When the total phenolic content (TPC) and antioxidant activity of sea buckthorn juice were assayed by spectrophotometry, the reaction solutions were not clarified, so centrifugation or membrane treatment was needed before determination. In order to find a suitable method for determining TPC and antioxidant activity, the effects of centrifugation and nylon membrane treatment on the determination of TPC and antioxidant activity in sea buckthorn juice were studied. TPC was determined by the Folin-Ciocalteau method, and antioxidant activity was determined by DPPH, ABTS, and FRAP assays. For Treatment Method (C): the sample was centrifuged for 10 min at 10,000 rpm and the supernatant was taken for analysis. Method (CF): The sample was centrifuged for 10 min at 4000 rpm, filtered by Nylon 66 filtration membranes with pore size of 0.22 μm, and taken for analysis. Method (F): the sample was filtered by Nylon 66 filtration membranes with pore size of 0.22 μm and taken for analysis. Method (N): after the sample of ultrasonic extract solution reacted completely with the assay system, the reaction solution was filtered by Nylon 66 filtration membranes with pore size of 0.22 μm and colorimetric determination was performed. The results showed that centrifugation or transmembrane treatment could affect the determination of TPC and antioxidant activity of sea buckthorn juice. There was no significant difference ( p > 0.05) between methods (CF) and (F), while there was a significant difference ( p < 0.05) between methods (C) (F) (N) or (C) (CF) (N). The TPC and antioxidant activity of sea buckthorn juice determined by the four treatment methods showed the same trend with fermentation time, and the TPC and antioxidant activity showed a significant positive correlation ( p < 0.05). The highest TPC or antioxidant activity measured by method (N) indicates that method (N) has the least loss of TPC or antioxidant activity, and it is recommended for sample assays.