The spectroscopic ptychography method, a technique combining X-ray ptychography imaging and X-ray absorption spectroscopy, is one of the most promising and powerful tools for studying the chemical states and morphological structures of bulk materials at high resolutions. However, this technique still requires long measurement periods because of insufficient coherent X-ray intensity. Although the improvements in hardware represent a critical solution, breakthroughs in software for experiments and analyses are also required. This paper proposes a novel method for restoring the spectrum structures from spectroscopic ptychography measurements with reduced energy points, by utilizing the Kramers–Kronig relationship. First, a numerical simulation is performed of the spectrum restoration for the extended X-ray absorption fine structure (EXAFS) oscillation from the thinned theoretical absorption and phase spectra. Then, this algorithm is extended by binning the noise removal to handle actual experimental spectral data. Spectrum restoration for the experimental EXAFS data obtained from spectroscopic ptychography measurements is also successfully demonstrated. The proposed restoration will help shorten the time required for spectroscopic ptychography single measurements and increase the throughput of the entire experiment under limited time resources.