The Santos Basin, located in the southeastern waters of Brazil, is a passive continental margin basin with the most abundant deepwater petroleum resources in the world discovered to date. However, few studies have been conducted on the present geothermal fields of the Santos Basin, which severely restricts the oil and gas resource evaluation of the basin. This study first utilizes 35 temperature data from 16 post-salt drilling wells and 370 temperature data from 31 pre-salt drilling wells to calculate the post-salt and pre-salt geothermal gradients and terrestrial heat flows in the Santos Basin. Then, the basin simulation software BasinMod 1D is used to quantitatively evaluate the impacts of salt rock sedimentation on the present geothermal fields and the maturity of pre-salt hydrocarbon source rocks. The results demonstrate that the present post-salt geothermal gradient in the Santos Basin is 2.20–3.97 ℃/100m, with an average value of 2.99 ℃/100m, and the post-salt terrestrial heat flow is 54.00-97.32 mW/m2, with an average value of 73.36 mW/m2, while the present pre-salt geothermal gradient is 2.21–2.95 ℃/100m, with an average value of 2.53 ℃/100m, and the pre-salt terrestrial heat flow is 61.85–82.59 mW/m2, with an average value of 70.69 mW/m2. These values are characteristic of a low-temperature geothermal fields in a zone with a stable structure. The sedimentation of the salt rock causes a decrease in the temperature of the pre-salt strata, which inhibits pre-salt hydrocarbon source rock maturity, with an inhibition rate of up to 1.32%. The inhibition degree decreases with increasing salt rock thickness. At the same time, the salt rock thickness is positively correlated with the present surface heat flow. The unique distribution of the salt rock and related salt structures lead to present terrestrial heat flow differences among different structural units in the basin. This study is of great significance for evaluating and exploring the pre-salt oil and gas resources in the Santos Basin.