Cnidium officinale is an important medicinal crop grown in Asia for its pharmacological properties. In this study, tetraploid breeding was conducted to increases the content of medicinal compound and tolerance to the environmental conditions using in vitro shoot culture of C. officinale. For this, we generated tetraploid C. officinale plants using oryzalin, a chromosome doubling agent, and compared the morphological traits, cytological characteristics, and heat stress-responsive gene expression levels between tetraploid and diploid genotypes. Chromosome doubling efficiency was the highest in plantlets treated with 4.0 mg∙L−1 oryzalin for 2 days. Compared with diploids, the plant height of tetraploids was reduced, while the petiole diameter was increased by approximately 39%. The dry matter of tetraploid leaves was significantly higher than that of diploid leaves. Compared with diploids, tetraploids showed higher chloroplast number and stomatal complex size but lower chlorophyll and carotenoid contents. The phenolic content of tetraploid plantlets was significantly higher than that of diploid plantlets. Contents of naringin as well as salicylic acid and gentisic acid, which are strong antioxidant compounds, were dramatically increased upon tetraploidization. Interestingly, liquid chromatography–mass spectrometry (LC–MS) analyses revealed increased levels of senkyunolide F and phthalide in tetraploid roots but not in tetraploid or diploid leaves.