Dye is an anionic common pollutant in industrial wastewater and poses a great threat to the environment and human health. Owing to its advantageous adsorption capacity, nanocellulose is widely used for wastewater treatment. The cell walls of Chlorella mainly comprise cellulose instead of lignin. In this study, residual Chlorella-based cellulose nanofiber (CNF) and cationic cellulose nanofiber (CCNF) with surface quaternization were prepared through homogenization. Moreover, Congo red (CR) was used as a model dye to measure the adsorption capacity of CNF and CCNF. The adsorption capacity was almost saturated when CNF and CCNF contacted CR for 100 min, and the adsorption kinetics coincided with the pseudo-secondary kinetics model. The initial concentration of CR considerably affected its adsorption on CNF and CCNF. Below the initial concentration of 40 mg/g, the adsorption on CNF and CCNF considerably increased with the increase in the initial concentration of CR. Based on the sorption isotherms analysis of CNF and CCNF, the Langmuir model fitted best with the experimental data. Thus, CNF and CCNF surfaces were uniform, and monolayer adsorption occurred. The adsorption of CR on CNF and CCNF was greatly affected by the pH value, and the acidic medium favored the adsorption of CR (especially for CCNF). CCNF showed a more advantageous adsorption capacity, with a maximum value of 1657.89 mg/g, compared to that of CNF (190.0 mg/g). According to the findings of this study, residual Chlorella-based CCNF could be a very promising adsorbent candidate for removing anionic dyes from wastewater.