Infrared technology has brought a quantum leap in the specialization of non-destructive systems for internal quality inspection of agricultural and food products. Applying near-infrared spectroscopy technique (NIRs) for tracking and estimating some antioxidants such as (Lycopene, β-carotene, Phytoene and Phytofluenxe) in tomato fruit fractions (Exocarp, Mesocarp, Endocarp and Tomato pomace) with prediction model. High-performance liquid chromatography (HPLC) device showed the antioxidant concentrations values within tomato fractions. Where, the maximum and minimum values observed in the mesocarp and exocarp fractions. Also, tomato fractions color analysis confirmed these results. Meanwhile, mesocarp fraction within range dark red color with h°≈ 31.7°, due to increased lycopene concentration, whereas, exocarp fraction was 77.29° for h°, within yellow range. In addition to HPLC and color reference methods were consensus significantly with the different of spectral transformations by the regression of partial least square (PLS). NIR spectra and antioxidant in tomato fractions were taken to establish calibration models for tracking and estimating antioxidant in tomato fractions by using partial least squares (PLS) model. The obtained Coefficients of prediction model (R2p) were 0.95, 0.91, 0.93 and 0.94 for Lycopene, β-Carotene, Phytoene and Phytofluenxe respectively. The values of (RPD) ratio obtained from the standard deviation to the standard error of prediction and also (RER) obtained from the standard error range of prediction model were varied for different tomato fractions and antioxidant content, and found that the NIR model suitable not only for screening the different concentrations values of antioxidants for tomato fractions, but also suitable for most applications including quality assurance.