The Erdaoqiao area has been the hot area of geothermal resource prospecting in southwestern China. Significance difference of scaling potential has been found between left and right riverbanks of the Erdaoqiao area. However, there still has no interpretation for the scaling difference since the genetic mechanism of geothermal waters remains unclear. In this study, hydrochemical, D–O–Sr isotopic and electromagnetic (EM) approaches were integrated to clarify the genetic mechanism and quantitively evaluate scaling potential of geothermal waters. All geothermal waters belonged to Ca–Na–HCO3 type and were determined by the weathering and/or dissolution of carbonates (66.87%) and silicates (31.53%) with cation exchange based on hydrochemical and Sr isotopic analyses. Na–K–Mg triangle diagram indicated they were immature water mixed by shallow cold water. Quartz geothermometer indicated the shallow reservoir temperatures (after cold–water mixing) of left riverbank (88.46 °C–90.51 °C) were higher than those of right riverbank (61.20 °C–87.89 °C). Silica – Enthalpy methods revealed the initial geothermal reservoir temperatures and cold-water mixing ratio were 102.03 °C–138.93 °C and 65.24%–85.87% in the right riverbank, 144.11 °C–146.76 °C and 73.08%–74.79% in the left riverbank of the Erdaoqiao area. D-O isotopes proposed the geothermal waters were recharged by atmospheric precipitation in the elevation of 4957 m to 5118 m. Therefore, the genetic model of geothermal waters in the Erdaoqiao area can be constructed. Stronger calcite scaling in left riverbank was attributed to deeper circulation identified by higher reservoir temperature and electromagnetic exploration. Quantitively evaluation demonstrated that the weight of scaling during 48 h in left riverbank (2968 kg) was four times higher than that in right riverbank (748 kg). The achievements of this study contribute to geothermal exploration in the Erdaoqiao and other similar areas worldwide.