Forest canopy height data are essential to assessing forest biomass and carbon storage, and they can be efficiently retrieved using the Advanced Terrain Laser Altimetry System (ATLAS) onboard ICESat-2. However, due to the sparse and discrete distribution of ATLAS footprints, the wall-to-wall mapping of forest canopy heights requires a combination of other ancillary data. In order to match the ATLAS data with ancillary data, or estimate higher-resolution canopy heights, the standard ATLAS canopy height products (ATL08), reported at a fixed step size of 100 m (12 m × 100 m), are typically divided into 30 m step sizes. There is little concern about the accuracy of the generated 30 m segment (12 m × 30 m) dataset. Furthermore, previous studies have primarily evaluated the along-track performance of the canopy height product, rather than the ability of ATLAS to provide an accurate representation of canopy heights at the pixel-wise level. In this study, we use airborne LiDAR data as references with which to evaluate the along-track accuracy of 30 m segment canopy height products and their accuracy in representing canopy height at the pixel-wise level. A framework method for spatially matching ATLAS canopy height estimate data with ancillary data accurately is also established in this study. This enables the use of ATLAS data to characterize pixel-wise canopy heights more precisely. The results show that the accuracy of the 30 m segment version dataset in representing the pixel-wise canopy heights (R² = 0.38, RMSE = 8.37 m) is lower than its along-track accuracy (R² = 0.44, RMSE = 7.63 m). Using only the nighttime data for the Taranaki region, the proposed method improves the estimation of pixel-wise forest canopy heights, with the R² increasing from 0.49 to 0.59, the RMSE decreasing from 7.48 m to 5.51 m, and the %RMSE decreasing from 36.7% to 27.6%. This study contributes to understanding the accuracy of the ATLAS in reflecting pixel-wise canopy height and provides a new way of spatially matching ATLAS canopy height data with other remote sensing data.