Three-dimensional (3-D) geometry information is valuable for fruit quality evaluation. This study was aimed at exploring an emerging structured -illumination reflectance imaging (SIRI) system, coupled with phase analysis, for reconstructing surface profiles of fruit. Phase-shifted sinusoidal patterns, distorted by the fruit geometry, were acquired and processed through phase demodulation, phase unwrapping and other post-processing procedures to obtain phase difference maps relative to the phase of a reference plane. The phase maps were then transformed into height profiles based on phase-to-height calibrations. A reference plane-based approach, in conjunction with the curve fitting technique using polynomials of order 3 or higher, was utilized for phase-to-height calibrations, which achieved superior accuracies with the root-mean-squared errors (RMSEs) of 0.027-0.033 mm for a height measurement range of 0-91 mm. The 3rd-order polynomial curve fitting technique was further tested on two reference blocks with known heights, resulting in relative errors of 3.75% and 4.16%. Tests of the calibrated system for reconstructing the surface of apple samples showed that surface concavities (i.e., stem/calyx regions) could be readily discriminated from bruising defects from both the phase difference images and reconstructed height profiles. This study has laid a foundation for using SIRI for reconstructing the 3-D geometry, and thus expanded the capability of the technique for quality evaluation of horticultural products. Further research is needed to utilize the phase analysis techniques for detecting surface concavities of apples, and optimize the phase demodulation and unwrapping algorithms for faster and more reliable detection. Published by Elsevier Ltd.