In this paper, a PtPd NC catalyst with a network structure of nanochains was prepared with KBr as a structure-directing agent, NaBH4 as a reducing agent, and modified multi-walled carbon nanotubes (MWCNTs) as a support. The experimental results show that the structure-directing agent KBr helps to form a particular type of nanochain with a network topology. PtPd NCs with various ratios (Pt:Pd = 2:1, 1:1, 1:2) have respective diameters of 30 nm, 35 nm, and 23 nm. With numerous structural flaws at the junctions, the nanochains’ distinctive network structure increases the number of active sites on the PtPd nanocenter surface. Electrochemical characterization results show that the current density of the PtPd NCs is about 658.5 mA mg−1, 1.5-times that of the Pt/C catalyst and 3.9-times that of the commercial Pd/C catalyst. Furthermore, it has better electrocatalytic stability for methanol oxidation than Pd/C and Pt/C catalysts.