Plant height (PH) is a crucial trait determining the plant architecture in chrysanthemum. To better understand the genetic basis of PH, we investigated the variations of PH, internode number (IN), internode length (IL), and stem diameter (SD) in a panel of 200 cut chrysanthemum accessions. Based on 330,710 high-quality SNPs generated by genotyping-by-sequencing (GBS), a total of 42 associations were identified via a genome-wide association study (GWAS), and 16 genomic regions covering 2.57 Mb of the whole genome were detected through selective sweep analysis. In addition, two SNPs, Chr1__339370594 and Chr18__230810045, respectively associated with PH and SD, overlapped with the selective sweep regions from Fst and π ratios. Moreover, candidate genes involved in hormones, growth, transcriptional regulation, and metabolic processes were highlighted based on the annotation of homologous genes in Arabidopsis and transcriptomes in chrysanthemum. Finally, the genomic selection (GS) for four PH-related traits was performed using a ridge regression best linear unbiased predictor model (rrBLUP) and six marker sets. The marker set constituted the top 1000 most significant SNPs identified via GWAS showed higher predictabilities for the four PH-related traits, ranging from 0.94 to 0.97. These findings improve our knowledge of the genetic basis of the PH and provide valuable markers that could be applied in chrysanthemum GS breeding program.