In view of the limitations of biochar made from single raw materials (crop straw-based biochar is relatively nutrient-poor, and pig manure-based biochar poses a risk of heavy metal accumulation), Co-pyrolyzed Biochar(CPB) was innovatively prepared through co-pyrolysis of straw and pig manure. The results showed that the specific surface area of CPB attained 21.58 m²/g, which was a substantial increase compared to that of Pig Manure-based Biochar (PMB) at 8.54 m²/g. Meanwhile, the contents of nitrogen, phosphorus, and potassium in CPB were all higher than those in Crop Straw-based Biochar (CSB), especially the phosphorus and potassium contents which increased by 262.30% and 282.70%, respectively. This study systematically and comprehensively explored the effects of CPB on soil fertility, enzyme activity, and rice growth in paddy fields. The research results indicated that CPB successfully integrated the high specific surface area of straw (21.58 m²/g) with the abundant mineral nutrients of pig manure(phosphorus content of 18.55 g/kg and potassium content of 33.56 g/kg). Moreover, its heavy metal content was significantly lower than that of PMB, with the contents of cadmium and arsenic decreased by 41.90% and 28.00%, respectively. Among the various application rates, the 2% application rate(CPB2) had the most remarkable effects: the contents of available phosphorus and rapidly available potassium in the soil increased significantly by 74.82% and 72.83%, respectively, compared to the control (CK, 0); the contents of organic matter and total nitrogen increased by 12.70% and 9.49%, respectively; the activities of soil phosphatase and catalase increased by 51.19% and 23.34%, respectively; and the rice yield increased by 8.37% compared to CK. Evaluation using the Integrated Fertility Index (IFI) revealed that the CPB2 treatment upgraded the soil fertility grade from Grade Ⅲ (CK, IFI value of 0.56) to Grade Ⅱ (IFI value of 0.68), with rapidly available potassium being the key driving factor with a weight of 0.112. The results of heavy metal pollution assessment showed that the heavy metal contents in all treatment groups were lower than the national standards (cadmium content ≤ 0.60 mg/kg), and the Nemerow Pollution Index (Pollution Index, PI) values were all less than 0.70, indicating no pollution risk. However, the 3% application rate treatment(CPB3) had a significantly lower yield increase effect (3.59%) than the CPB2 treatment due to micropore blockage and nutrient competitive adsorption. This study confirmed that co-pyrolyzed biochar optimized the “nutrient-structure-enzyme activity” network system of soil through the “carbon-ash synergistic effect” (i.e., porous carbon structures loading mineral nutrients). Among them, the 2% application rate was the optimal threshold for achieving “high yield-low risk” in paddy field systems.