This study combined three-dimensional (3D) printing and composite multiscale cross-sample entropy (CMSCE) in structural health monitoring (SHM) and explored a quantification criterion for single-story structural damage index (DI). By quantifying the DI, the study established a SHM system suitable for real-world structures. A numerical model of a seven-story 3D printed structure was first created. Through the establishment of various bracing conditions as failure modes, damage to the structure was simulated properly, and CMSCE was used to effectively indicate the location of damage. Moreover, the DI was used to shorten the assessment time and improve system accuracy. The DI quantification facilitated observation of the effects of various degrees of damage on the analysis results. Based on the results, an experiment involving a 3D-printed structure was conceived. First, an experiment involving a seven-story structure with severe, moderate, and marginal single-story damage was conducted. The signals obtained from these structures were used to perform CMSCE analysis. Structural damage was detected using entropy curves and DI figures to determine the location and degree of damage as well as to quantify the DI. Thus, the study developed a reliable method by combining emerging 3D printing technology with the CMSCE DI to explore the feasibility of practical application.