To decrease the 5-hydroxymethyl-2-furancarboxylic acid (HMFCA) bioconversion cost, an optimized strategy for HMFCA production from agriculture wastes were established in this study. Corncob residue (CCR) and soybean dreg were hydrolyzed by Pseudomonas aeruginosa PC-1 as substitutes for the traditional nutrient sources. A 5-hydroxymethylfurfural (HMF) conversion of 100% and an HMFCA yield of 83.5% were obtained from 15% soybean dreg and 5% CCR with 10 FPU/g cellulase. The addition of 0.2 g/L of the surfactant rhamnolipid reduced the cellulase usage by 25% and increased the HMFCA yield to 86.1%. An excellent HMFCA yield of 808.9 mM was obtained within 62 h in the presence of a 900 mM HMF substrate via the fed-batch strategy. Notably, the material cost of HMFCA using this strategy was estimated to be only 11.47% of the traditional method. This study provides a new and low-cost strategy for the large-scale industrial production of HMFCA.