This study investigates the effects of various treatments on soil pH, SOC, and crop yield in red soil with a pH of 4.25 through a two-year field experiment, using a rapeseed and sesame cropping system. The treatments included the control (CK); lime (CaO) (L); fully fermented pig manure (M); a calcium–magnesium–phosphate fertilizer (P); lime and fully fermented pig manure (LM); lime and the calcium–magnesium–phosphate fertilizer (LP); fully fermented pig manure and the calcium–magnesium–phosphate fertilizer (MP); and lime, fully fermented pig manure, and the calcium–magnesium–phosphate fertilizer (LMP). Then, the changes in yield, soil pH, and SOC were analyzed. The results showed that, among all treatments, the LMP treatment produced the highest yields for both rapeseed (93.62%) and sesame (45.10%); they increased by 93.62% and 45.10% compared with that for CK. Furthermore, these treatments with lime application increased the soil pH. During the rapeseed season, compared with CK, the soil pH values increased by 0.87, 0.75, 0.90, 1.03, 1.24, 1.18, and 1.45 units in the L, M, P, LM, LP, MP, and LMP treatments, respectively. Moreover, they increased by 0.66, 0.34, 0.51, 0.95, 0.82, 0.72, and 1.03 units, respectively, in the sesame season. Similarly, in terms of yield, the highest pH was observed in the LMP treatment for both the rapeseed and sesame seasons. In contrast to soil pH, the effects of these treatments on SOC were less pronounced. Furthermore, the relationship between soil pH and crop yields was significant (R2, p < 0.05). In addition, fitted equations indicated a higher yield response (5.17%) in rapeseed compared with that in sesame (2.32%), while soil pH increased by 0.1 unit. Therefore, the combined application of lime, composted pig manure, and calcium–magnesium–phosphate is an effective strategy to reduce soil acidification and improve crop yield in highly acidified red soils, with the increase in soil pH having a more substantial impact on crop yield than the increase in SOC.