Idesia polycarpa from Sichuan is a valuable germplasm with high economic potential, but it faces variety scarcity. To address this, this study collected 16 varieties (lines), identifying IpHT1 as a promising parent due to its high oil content (38.5%) and red fruits. Polyploid induction via adding 0.50% colchicine to Murashige and Skoog (MS) medium yielded 520 IpHT1 mutagenized seedlings. Subsequently, flow cytometry (FCM) was performed on 401 morphologically variant seedlings which had been initially screened, resulting in the identification of 15 suspected triploids, 35 suspected tetraploids, and 3 chimeras. Furthermore, fluorescence in situ hybridization (FISH) analysis found that the probe (AG3T3)3 had terminal signals at both ends of each chromosome, allowing for the counting of 42 chromosomes in diploids and 84 in tetraploids. The probe 5S rDNA showed 2, 3, and 4 hybridization signals in the interphase nuclei of diploid, triploid, and tetraploid cells, respectively, but the probe (GAA)6 failed to produce any signal on I. polycarpa chromosomes. Ultimately, 18 polyploids were selected, including 7 triploids and 11 tetraploids. Triploids and tetraploids showed significant leaf morphological and physiological differences from diploids. Consequently, this study successfully established a polyploid breeding system for I. polycarpa, thereby enhancing its genetic diversity and breeding potential.