This study aims to investigate the effects of different hydroxy-terminated silicones on the properties of polycarbonate-silicone copolymers (ICS-PC) by introducing flexible and hydrophobic silicone into isosorbide-based polycarbonate through melt transesterification- polycondensation method. Through compatibility and transesterification experiments, it is confirmed that the alcohol-hydroxyl polydimethylsiloxane (a-PDMS) has higher reactivity and silicone conversion than the phenol-hydroxyl polydimethylsiloxane (p-PDMS), but the conversion does not exceed 81%. Polyether-modified silicone (PEMS) exhibits better compatibility and higher reactivity, thus resulting in higher conversion that can reach 86%. Effects of the type and content of silicone on the glass transition temperature (Tg), optical transparency, saturated water absorption, and mechanical strength of ICS-PCs were also discussed. It is found that p-PDMS has higher Tg, hydrophobicity, and mechanical strength with similar silicone content, but the total transmittance does not exceed 60%. In contrast, the PEMS system exhibits better optical transparency due to its improved compatibility with the PC matrix, with a total transmittance of up to 73%, Tg exceeding 150 °C while maintaining excellent flexibility and hydrophobicity. These results are helpful to further improve the comprehensive properties of bio-based polycarbonates.