Bottle gourd [Lagenaria siceraria (Mol.) Standl.] is one of the most common horticultural and medicinal crops. Genetic transformation is a rate-limiting step in unraveling the function of genes and molecular breeding in this non-model crop. In this study, we established an optimized protocol for transformation using a seed germination pouch as a growth carrier and developed bottle gourd composite plants. Overground explants were inoculated with Agrobacterium rhizogenes strain R1000, which harbored a binary vector pBI121 carrying the GUS reporter gene. The integration of GUS into transgenic roots was confirmed via reverse transcription-polymerase chain reaction and histochemical staining. Furthermore, we screened for desirable genotypes from 14 bottle gourd germplasm collections based on the number of induced roots, transformation efficiency, and induction rate, and “Changguang” (transformation efficiency, approximately 36.8%) was selected as the genotype suitable for hairy root induction in bottle gourd. The optimized protocol presented here is a rapid, suitable, and efficient tool for studying the function of genes and root biology of bottle gourd in the future.