High-throughput measurement of plant photosynthesis ability presents a challenge for the breeding process aimed to improve crop yield. As a novel technique, hyperspectral lidar (HSL) has the potential to characterize the spatial distribution of plant photosynthesis traits under less confounding factors. In this paper, HSL reflectance spectra of maize leaves were utilized for estimating the maximal velocity of Rubisco carboxylation (Vcmax) and maximum rate of electron transport at a specific light intensity (J) based on both reflectance-based and trait-based methods, and the results were compared with the commercial Analytical Spectral Devices (ASD) system. A linear combination of the Lambertian model and the Beckmann law was conducted to eliminate the angle effect of the maize point cloud. The results showed that the reflectance-based method (R2 ≥ 0.42, RMSE ≤ 28.1 for J and ≤4.32 for Vcmax) performed better than the trait-based method (R2 ≥ 0.31, RMSE ≤ 33.7 for J and ≤5.17 for Vcmax), where the estimating accuracy of ASD was higher than that of HSL. The Lambertian–Beckmann model performed well (R2 ranging from 0.74 to 0.92) for correcting the incident angle at different wavelength bands, so the spatial distribution of photosynthesis traits of two maize plants was visually displayed. This study provides the basis for the further application of HSL in high-throughput measurements of plant photosynthesis.