Soil organic carbon (SOC) and nitrogen (N) fractions greatly affect soil health and quality. This study explored the effects of wheat straw incorporation on Chinese rice paddy fields with four treatments: (1) a control (CK), (2) a mineral NPK fertilizer (NPK), (3) the moderate wheat straw (3 t ha−1) plus NPK (MSNPK), and (4) the high wheat straw (6 t ha−1) plus NPK (HSNPK). In total, 0–5, 5–10, 10–20, and 20–30 cm soil depths were sampled from paddy soil in China. Compared with the CK, the HSNPK treatment (p < 0.05) increased the C fraction content (from 13.91 to 53.78%), mainly including SOC, microbial biomass C (MBC), water-soluble organic C (WSOC), and labile organic C (LOC) in the soil profile (0–30 cm), and it also (p < 0.05) increased the soil N fraction content (from 10.70 to 55.31%) such as the soil total N (TN) at 0–10 cm depth, microbial biomass N (MBN) at 0–20 cm depth, total water-soluble N (WSTN) at 0–5 and 20–30 cm depths, and total labile N (LTN) at 0–30 cm depth. The primary components of soil LOC and LTN are MBC and MBN. Various soil C and N fractions positively correlated with each other (p < 0.05). The HSNPK treatment promoted the soil MBC, WSOC, and LOC to SOC ratios, and also promoted MBN, WSTN, and LTN to soil TN ratios at a depth of 0–20 cm. To summarize, the application of HSNPK could maintain and improve rice paddy soil quality, which leads to increased rice grain yields.