The transport properties of warm dense neon (Ne) and krypton (Kr) are studied by combining self-consistent fluid variational theory (SFVT) with linear response theory (LRT). The components are determined using the SFVT, and the transport parameters, including the electrical conductivity, thermal conductivity, and thermopower, are calculated with the LRT. The relevant scattering mechanisms, including electron-ion, electron-electron, and electron-atom scatterings, are taken into account. An effective potential model in combination with the Muffin-tin model is introduced to further improve the description for electron-atom scattering, which not only includes static, exchange, and polarization interactions but also considers the plasma environmental effects. It is found that for electron-atom scattering, the influence of the plasma density is significant at lower scattering energies but the effects are different for electron-Ne and electron-Kr scattering. For electron-Kr scattering, a plasma density-dependent Ramsauer-Townsend minimum is observed. The obtained transport parameters are compared with the available experiments and other simulations. The plasma phase transition of warm dense Kr is revisited from multiple perspectives based on the numerical simulation results for the electrical conductivity and thermopower. These observations may help one to better understand the transport properties of warm dense noble gases and are an important guide for future experimental designs and theoretical developments.