Carboxymethyl-quaternized oligochitosan (CMQAOC) was prepared through carboxymethylization and N-quaternization of oligochitosan (OC) which was obtained from chitosan degradation. The structure was confirmed by Fourier transform infrared spectroscopy (FT-IR), 1H-NMR, and X-ray diffraction (XRD) analysis. The performances for both scale and microbial inhibition of CMQAOC were evaluated by static test and culture flask method, respectively. The results showed that the scale inhibition rate for calcium carbonate and calcium sulfate scale were both beyond 80% with a CMQAOC dosage of 20 mg/L. With a degree of substitution for quaternary ammonia of up to 0.74, the killing rate for saprophytic bacteria and sulfate-reducting bacteria was 98.9 and 100%, respectively. The ratio of biochemical oxygen demand/chemical oxygen demand (BOD5/COD) of CMQAOC was 0.45, showing that CMQAOC is as biodegradable as OC.