Single-walled carbon nanotubes (SWCNTs) functionalized with sparse surface chemical groups are promising for a variety of optical applications such as quantum information and bio-imaging. However, the luminescence efficiencies and stability, two key aspects, undoubtedly govern their practical usage. Herein, we assess the surface migration of oxygen and triazine groups on as-modified SWCNT fragments by adopting transition state theory and explore the de-excitation of oxygen-functionalized SWCNT fragments by performing non-adiabatic excited-state dynamics simulations. According to the predicted moderate or even small reaction barriers, the migration of both oxygen and triazine groups is feasible from an sp3 defect configuration forming an energetically more stable sp2 configuration at moderate or even room temperatures. Such isomerization leads to drastically different light emission capabilities as indicated by the large or zero oscillator strengths. During the dynamics simulations, the lowest excited singlet (S1) state rapidly decays in energy within 20 fs and then fluctuates until the end, providing insights into the emission mechanism of SWCNTs. This study highlights the potential intrinsic limitations of surface-functionalized SWCNTs for luminescence applications.