Due to the essential role of nano-fertilizers in crop production, studies have yet to be conducted to evaluate nano-molybdenum (Mo) application on winter wheat (Triticum aestivum L.). The present study assessed the efficacy of nano-Mo on the Mo-uptake, plant growth, and winter wheat yield. Wheat was grown in the pot experiment using four experimental groups (deionized water: C, nano potassium molybdate: NMoK, potassium molybdate: MoK, and ammonium molybdate: MoA), each with six replicate samples applied-foliar three times in a 30-day interval. The results revealed that NMoK improved Mo accumulation in grains, stomatal conductance, root dry weight, yield, and the number of spikes per pot of wheat compared with MoK. Additionally, NMoK treatment significantly increased wheat grain yield by 46.29%, 13.94%, and 17.70% compared with C, MoK, and MoA treatments, respectively. These results demonstrated that the nano-Mo application may enhance Mo-inefficient wheat growth, thus, increasing its productivity under acidic soil conditions. The principal component analysis (PCA) elucidates that all variables reside within the positively correlated variable domain. This encompasses parameters related to yield, photosynthetic machinery, and Mo uptake by various plant organs. Through cluster analysis, the nano-Mo group exhibited a more pronounced influence on the variables than the without-Mo and non-nano-Mo groups. Based on our findings, nano-Mo could be a suitable alternative to non-nano molybdenum fertilizers. This recommendation is particularly relevant for enhancing the growth of winter wheat crops cultivated in acidic soil conditions.