To enhance the electrocatalytic performance of a flexible Pd@CFs catalyst for methanol oxidation, deep cryogenic treatment in liquid nitrogen was introduced. The effects of the frequency and time of the deep cryogenic treatment on the surface crystal orientation, microstructure morphology, mechanical performance, and electrocatalytic performance for methanol oxidation were studied. The results showed that when the frequency of the deep cryogenic treatment was 2 times and the deep cryogenic time was 24 h, the electrocatalytic performance of the catalyst was the best. Compared with the catalyst without deep cryogenic treatment, the activity and stability of the catalyst increased by about 33% and 41%, respectively. The activity and stability of the catalyst were about 43.4 times and 6.3 times that of the commercial Pd/C catalyst, respectively. After 500 cycles of CV testing, the performance of the catalyst decay rate was only 3.9%. Compared to the CFs, the tensile strength and the elongation rates of the catalyst increased by 24.6% and 57%, respectively. This is due to deep cryogenic treatment causing Pd grains to rotate from a disordered arrangement to an ordered arrangement, making the metal particles more dispersed and exposing more active sites, ultimately improving the electrocatalytic oxidation ability of methanol. The excellent electrocatalytic efficiency of Pd@CFs-24-2 coupled with its simple and easy preparation method has great potential for promoting the development of DMFCs.