Two-way satellite time and frequency transfer (TWSTFT) using satellites in inclined geo-synchronous orbit (IGSO) is fundamentally more difficult than using satellites in geostationary orbit (GEO), due to the fact that IGSO satellites are constantly moving relative to a ground station, which brings in large residual effects. In this paper, we designed a protocol and an algorithm to correct several factors that affect the precision of TWSTFT using IGSO satellites. We used two ground stations, each equipped with sending and receiving channels, to conduct real-time measurements of the distance and the speed of an IGSO satellite, and data collected were used to make appropriate corrections. We tested this concept by conducting TWSTFT experiments using an IGSO satellite (BEIDOU I1-S), and compared the results with that obtained using a GEO satellite (CHINASAT 12). Indeed, the individual components that contribute to the residual effects of TWSTFT measurements using the IGSO satellite were several orders of magnitude greater than that of the GEO satellite. By using our modified protocol, TWSTFT results with an IGSO satellite were well accorded with that of using a GEO satellite; the standard deviation of residuals was less than 0.4 ns, well within the limit for the measurement uncertainty of TWSTFT. Therefore, we have expanded the use of IGSO satellites for TWSTFT. In principle, it should also be applicable to medium earth orbit and other satellites.