Electrohydrodynamic (EHD) embedded printing technology offers notable advantages in non-contact printing of low-viscosity inks, including one-step manufacturing, liquid encapsulation, and higher print resolution. By incorporating a liquid substrate, this technology stabilizes the printing process, enhances overall print quality, and mitigates issues such as the coffee ring effect. Despite these benefits, printability challenges remain, primarily due to interference from residual charges and the complex solute migration influenced by ink rheology. To address these, this study employed pulse signal modulation, successfully neutralizing residual charges and enhancing printing process stability. Additionally, key EHD printing parameters—pressure, printing height, and voltage—were optimized to further improve reliability and printability. The study also delved into the impact of ink rheology on printed structure morphology and, consequently, on the embedded morphology. Specifically, it analyzed how variations in rheological properties of low-viscosity inks influenced the printed structure, which in turn affected the final embedded morphology. A comprehensive mapping of these influences was developed, revealing correlations between printed structure morphology and embedded morphology. This work provides a comprehensive process guide that helps optimize printability and ink rheology in EHD embedded printing, thereby enhancing its potential for one-step manufacturing of flexible electronics and expanding its potential applications to high-precision embedded printing of other functional materials.