In this work, the adsorption behavior of dodecylamine (DDA) on scheelite and calcite mineral surfaces were investigated by molecular dynamics (MD) simulation, zeta potential measurement, AFM observation, contact angle measurement, and flotation test. The results implied that, the different adsorption behavior of DDA on scheelite and calcite surfaces was mainly attributed to cationic species RNH3+ of DDA. The adsorption of neutral species RNH2 and complex precipitates produced by the reactions between RNH3+ and anionic species released by both mineral surfaces, also played important roles. In a DDA solution (1 × 10−4 mol/L, pH 7.5–8.0), a handful of RNH2 of DDA adsorbed on both scheelite and calcite surfaces through N–Ca bonding and hydrogen bonding between hydrogens of –NH2group and mineral surface oxygens. On positively charged calcite surface, RNH3+adsorbed on a moderate number of CO32− sites through electrostatic attraction and hydrogen bonding, which caused a moderate zeta potential increase for calcite. On negatively charged scheelite surface, a large number of cationic species RNH3+ could easily adsorb on abundant WO42− sites, which caused a significant increase of zeta potential for scheelite. The different adsorption behavior led to a heavier monolayer coverage of DDA species on scheelite surface, and thus a more hydrophobic surface and a better flotation recovery of scheelite. The present work helps propose a new adsorption model of DDA on scheelite and calcite.