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We renormalize the chiral effective field theory (EFT) potential in harmonic-oscillator (HO) model space. The low energy constants (LECs) are utilized to absorb not just the ultra-violet part of the physics due to the cutoff, but also the infrared part due to the truncation of model space. We use the inverse J-matrix method to reproduce the nucleon-nucleon (NN) scattering phase shifts in the given model space. We demonstrate that by including the NLO correction, the nucleon-nucleon scattering in the continuum could be well reproduced in the truncated HO trap space up to laboratory energy $T_{lab}=100$ MeV with number of HO basis $n_{max}$ as small as 10. A perturbative power counting starts at subleading order is adopted in this work, and how to extract the perturbative contribution is demonstrated. Our work serves as the input to perform ab-initio calculations.