Lignosulfonate (LS) is a by-product obtained during sulfite pulping process and is commonly used as a growth enhancer in plant growth. However, the underlying growth promoting mechanism of LS on shoot growth remains largely unknown. Hence, this study was undertaken to determine the potential application of eco-friendly LS chelated ion complex (NaLS and CaLS) to enhance recalcitrant indica rice MR219 shoot growth and to elucidate its underlying growth promoting mechanisms. The NaLS was shown to be a better shoot growth enhancer as compared to CaLS, with optimum concentration of 300 mg/L. Subsequent comparative proteomic analysis revealed an increase of photosynthesis-related proteins and stress regulator proteins abundance in NaLS-treated rice as compared to MSO (control). Consistently, biochemical analyses showed a significant increase of rubisco activity, total chlorophyll, total sugar and total protein contents in NaLS-treated rice, implying NaLS role in empowering photosynthesis activities that led to plant growth enhancement. In addition, low level of peroxidase activity, malondialdehyde content and phenylalanine ammonia lyase activity were also observed in NaLS-treated rice. These results suggest that NaLS plays a role in modulating cellular homeostasis to provide a conducive cellular environment for plant growth. Taken together, NaLS improved shoot growth of recalcitrant MR219 rice by upregulation of photosynthetic activities and reduction of cellular stress leading to better plant growth.