Rice straw is used as livestock feed and compost. Ferimzone and tricyclazole, common fungicides for rice blast control, can be found in high concentrations in rice straw after unmanned aerial vehicle (UAV) spraying, potentially affecting livestock and human health through pesticide residues. In this study, an optimized method for the analysis of the two fungicides in rice straw was developed using the improved QuEChERS method. After the optimization of water and solvent volume, extraction conditions including ethyl acetate (EtOAc), acetonitrile (MeCN), a mixed solvent, and MeCN containing 1% acetic acid were compared. Different salts, including unbuffered sodium chloride, citrate, and acetate buffer salts, were compared for partitioning. Among the preparation methods, the MeCN/EtOAc mixture with unbuffered salts showed the highest recovery rates (88.1–97.9%, RSD ≤ 5.1%). To address the severe matrix effect (%ME) of rice straw, which is characterized by low moisture content and cellulose-based complex matrices, samples were purified using 25 mg each of primary–secondary amine (PSA) and octadecylsilane (C18), without pesticide loss. The developed method was validated with a limit of quantification (LOQ) of 0.005 mg/kg for target pesticides, and recovery rates at levels of 0.01, 0.1, and 2 mg/kg met the permissible range (82.3–98.9%, RSD ≤ 8.3%). The %ME ranged from −17.6% to −0.3%, indicating a negligible effect. This optimized method was subsequently applied to residue studies following multi-rotor spraying. Fungicides from all fields and treatment groups during harvest season did not exceed the maximum residue limits (MRLs) for livestock feed. This confirms that UAV spraying can be safely managed without causing excessive residues.