In order to recycle the by-products of cellulose nanocrystals (CNCs) for resource utilization and reduce the application of chemical fertilizers, they were formulated into a rice greening and tillering fertilizer, and a field experiment was conducted in the soda saline alkali area of Daqing, Heilongjiang Province in 2023. The experiment set up four treatments, namely conventional nitrogen fertilizer treatment (CK), CNCs by-products+conventional nitrogen fertilizer treatment (A1), CNCs by-products+70% conventional nitrogen fertilizer treatment(A2), CNCs by-products+70% conventional nitrogen fertilizer treatment+500 mL/667 m² Bacillus velezensis bacterial liquid (A3). The yield and quality traits of conventional japonica rice variety Suijing 18 were measured under different treatments. The results indicated that the theoretical and actual yield of rice were in the order of A1>A3>CK>A2. The actual yield of rice in the A1 treatment increased by 26.17%, 39.23%, and 24.30% compared to CK, A2, and A3 treatments, respectively. Adding CNCs by-products could improve rice yield components, primary and secondary stem traits, and significantly enhance rice processing quality, but significantly reduce grain length, aspect ratio, protein content, and amylose content. Compared with A2 treatment, A3 treatment could significantly improve the spike weight, grain density, yield structure, secondary branch stalk setting, and processing quality of rice. All treatments had minimal effect on the cooking and eating quality of rice. This indicated that the combined use of CNCs by-products and Bacillus velezensis could enhance the efficiency of greening and tillering fertilizer, significantly improve rice yield and quality.