Diffuse transmittance spectra in the near-infrared scope as a prevalent sensitivity method carried out to test epidermal thickness of ‘Gannan’ navel oranges. In order to lay a good foundation for accurate and rapid online classification, variable selection methods was intervened for navel orange model optimization. In spectral range of 900–1650 nm, navel orange in thick skin depth chosen arbitrarily were set up the qualitative models for both calibration and prognostication sets in this experiment. Firstly, different pretreatment methods such as the Savitzky-Golay, the first derivative and so on were compared by PLS modeling results. Then GA and SPA were brought in to improve predictive models. Compared with results, light scattering can be effectively eliminated by the standard normal variate transformation (SNV). Moreover, fewer variables and model optimization were carried out by GA. The supreme calibration model procured with GA-PLS approach had the Rp of 0.864, RMSEP of 0.290, RC of 0.882 and RMSEC of 0.264. The experiment showed the detection of epidermal thickness of navel orange is completely feasible.