In-field Sound Speed Profile (SSP) measurement is still indispensable for achieving centimeter-level-precision Global Navigation Satellite System (GNSS)-Acoustic (GNSS-A) positioning in current state of the art. However, in-field SSP measurement on the one hand causes a huge cost and on the other hand prevents GNSS-A from global seafloor geodesy especially for real-time applications. We propose an Empirical Sound Speed Profile (ESSP) model with three unknown temperature parameters jointly estimated with the seafloor geodetic station coordinates, which is called the 1st-level optimization. Furthermore, regarding the sound speed variations of ESSP we propose a so-called 2nd-level optimization to achieve the centimeter-level-precision positioning for monitoring the seafloor tectonic movement. Long-term seafloor geodetic data analysis shows that, the proposed two-level optimization approach can achieve almost the same positioning result with that based on the in-field SSP. The influence of substituting the in-field SSP with ESSP on the horizontal coordinates is less than 3 mm, while that on the vertical coordinate is only 2–3 cm in the standard deviation sense.