Rational design of catalytic nanomaterials is essential for developing high-performance fuel cell catalysts. However, structural degradation and elemental dissolution during operation pose significant challenges to achieving long-term stability. Herein, the development of multi-grained NiPt nanocatalysts featuring an atomically ordered Ni₃Pt₅ phase within intragrain is reported. Ultrasound-assisted synthesis facilitates atomic transposition by supplying sufficient diffusion energy along grain boundaries, enabling unprecedented phase formation. The Ni₃Pt₅ embedded nanocatalysts exhibit outstanding proton exchange membrane fuel cell performance under both light-duty and heavy-duty vehicle conditions, with significantly reduced Ni dissolution. Under light-duty vehicle conditions, the catalyst achieves a mass activity of 0.94 A mg_Pt ^-1 and a 421 mA cm^-2 current density (@ 0.8 V in air), retaining 78% of its initial mass activity after long-term operation. Under heavy-duty vehicle conditions, the multi-grained nanocrystal demonstrates only an 8% decrease in Pt utilization, a 5% power loss, and a 13 mV voltage drop, surpassing U.S. Department of Energy (DOE) durability targets. This study underscores the critical role of the atomically ordered Ni₃Pt₅ phase in stabilizing multi-grained NiPt nanocrystals, enhancing both durability and catalytic activity. These findings establish Ni₃Pt₅ embedded nanocatalysts as promising candidate for next-generation PEMFC applications, addressing key challenges in long-term operation.