Polymers with integrated functions might have greater possibility to meet the various requirements for a specific application. This work demonstrates a molecule-design based development of multi-functional polymers with a branched polysiloxane polymer which exhibits integrated functions including good thermal stability, high thermal resistance, high flame retardancy and self-extinguishing properties, high transparency in the ultraviolet to blue light region, and relatively high RI value (1.59). This multi-functional polymer is potentially applicable in high performance LED encapsulants.