Non-crystal microporous starch (NCMS) containing microporous and amorphous structures was prepared from native corn starch by heat treatment and solvent exchange. NCMS can be used as fillers, coatings, and raw materials in the preparation of various denatured starch because of its specific surface area and amorphous region. However, the hydrophilicity of NCMS limits its applications in papermaking. Thus, in this study, NCMS was reacted with alkyl ketene dimer (AKD) to prepare hydrophobic NCMS (H–NCMS), which is more stable, and convenient for storage and use in surface sizing. The optimal preparation conditions were selected using single-factor tests. The product, which was prepared at 55 °C for 3 h with an AKD dosage of 80%, had a sizing degree of 67 s. Characterization by X-ray diffraction (XRD), scanning electron microscopy (SEM), and Fourier transform infrared (FT-IR) spectroscopy confirmed that NCMS, H–NCMS, and sized paper were obtained. The thermal stability and hydrophobicity of the paper were measured using thermogravimetric analysis (TGA) and water contact angles, respectively. The results indicated that the sized paper has excellent thermal stability and hydrophobicity after surface sizing with 0.9% H–NCMS. Food wrapping paper with excellent strength and hydrophobicity was successfully prepared using H–NCMS and ultrasonic-assisted wheat straw pulp (UWP).