This study aims to prepare natural biomass-based nonionic antimicrobial polymers with excellent biocompatibility, nonleachability, antimicrobial activity, and polymer miscibility. Two new cellulose-based nonionic antimicrobial polymers (MIPA and MICA) containing many terminal indole groups were synthesized using a sustainable one-pot method. The structures and properties of the nonionic antimicrobial polymers were characterized using nuclear magnetic resonance hydrogen spectroscopy ( 1 H NMR), infrared spectroscopy (FTIR), wide-angle X-ray diffractometry (XRD), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), scanning electron microscopy (SEM), gel chromatography (GPC), and other analytical techniques. The results showed that microcrystalline cellulose (MCC) molecules combined with indole derivatives through an esterification reaction to produce MICA and MIPA. The crystallinity of the prepared MICA and MIPA molecules decreased after MCC modification; their morphological structure changed from short fibrous to granular and showed better thermal stability and solubility. The paper diffusion method showed that both nonionic polymers had good bactericidal effects against the two common pathogenic bacteria Escherichia coli (E. coli, inhibition zone diameters >22 mm) and Staphylococcus aureus (S. aureus, inhibition zone diameters >38 mm). Moreover, MICA and MIPA showed good miscibility with biodegradable poly(vinyl alcohol) (PVA), and the miscible cellulose-based composite films (PVA-MICA and PVA-MIPA) showed good phase compatibility, light transmission, thermal stability (maximum thermal decomposition temperature >300 °C), biocompatibility, biological cell activity (no cytotoxicity), nonleachability, antimicrobial activity, and mechanical properties (maximum fracture elongation at >390%).