We investigated the shaft deformation due to hub press-fitting and disk clamping processes in a 2.5" hard disk drive (HDD). We measured the non-repeatable runout (NRRO) and the amplitude at the half speed whirl (HSW) frequency of the HDD spindle system with deformed shaft. We numerically analyzed the effect of deformed shaft on pressure and found that the upper grooved journal bearing has lower maximum pressure than the lower grooved journal bearing due to enlarged radial gap. Finally, we proposed a robust shaft design against shaft deformation to reduce NRRO. We confirmed that the proposed shaft design reduces overall NRRO and the amplitude at HSW frequency by 14.3 % and 63.7 %, respectively.