This study was designed to investigate the effects of different processing methods on the antioxidant and anti-cancer properties of soymilk crude phenolic extract (CPE) using the human prostate cancer cell line DU 145 as a model system. Four grinding methods and two ultra-high temperature (UHT) processing methods were investigated. Briefly, the four grinding methods included grinding with tap water (Method 1), okara-washed water (Method 2), soaked water (Method 3), as well as both okara-washed water and soaked water (Method 4); the two UHT processing conditions included one-phase UHT (143 °c, 60 s) and two-phase UHT (120 °C, 80 s + 140 °C, 4 s) methods. The antioxidant capability of CPE was measured by oxygen radical absorbance capacity (ORAC) and/or ferric reducing antioxidant power (FRAP) and 2, 2-diphenyl-1-picrylhydrazyl free radical scavenging activity (DPPH) assays. The DU 145 human prostate cancer cell line was sub-cultured in the presence of CPE at various concentrations (0, 1, 2, 4, 8 mg/ml) for 48 h and the percentage of cell viability was evaluated by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay and/or flow cytometric analysis with carboxyfluorescein succinimidyl ester (CFSE) staining. An induction of apoptosis was detected by flow cytometric analysis with annexin V/ propidium iodide (Pl) double staining, morphological change observation with acridine orange/ethidium bromide (AO/EB) double staining, and Western blot assay of apoptotic proteins. The results showed that grinding Method 4 and the two-phase UHT method exhibited greater total phenolic content and antioxidant capability than the other three grinding methods and one-phase UHT, respectively. In addition, soymilk CPE inhibited cell proliferation in a dose-dependent manner and upon purification. The anti-proliferation effects observed in soymilk CPE were associated with the apoptosis induction in DU 145 cell line as evidenced by morphological changes and the expression of apoptotic proteins. These results suggest that the soymilk CPE plays an important role in anti-proliferation, and apoptotic properties of soy in DU 145 cells. Furthermore, these health-promoting properties were affected by processing conditions, such as grinding and thermal conditions. The results of this study benefit the soy product industry to select appropriate processing conditions to retain more health-promotion phytochemicals during soy food's processing.