The presence of agricultural herbicides in the aquatic environment is one of the most important problems of water resource ecosystems. The present study was performed to remove 2,4-Dichlorophenoxyacetic acid and glyphosate herbicides from aqueous solutions by Thiol modified the magnetic mesoporous silica (magMCM-41) nanoparticles using extracted silica from rice husk ash, and the modification was performed by the 3-Mercaptopropyltrimethoxysilane (Thiol) functional group. The properties of the synthesized nanoparticles were investigated using XRD, FT-IR, TGA, VSM, pHZPC and TEM analyzes. The efficiency of the synthesized adsorbent was also studied by investigating the effect of pH, time, adsorbent dose, and initial concentrations of contaminants. The results of this study showed that the highest rate of elimination of 2,4-Dichlorophenoxyacetic acid and glyphosate was observed at herbicides the concentrations of 20 mg L−1, adsorbent dose of 0.2 gL−1, the contact time of 30 and 60 min and pH of 6 and 5 respectively. Under optimum conditions, 83.44 % and 79.38 % were removed for 2,4-Dichlorophenoxyacetic acid and glyphosate, respectively. Also, the adsorption capacity of SH-mgMCM-41 for 2,4-Dichlorophenoxyacetic acid and glyphosate is 120.36 and 108.53 mg/g, respectively. The results of the adsorption isotherms showed that the Langmuir model had a little better fit for 2,4-Dichlorophenoxyacetic acid and glyphosate with a correlation coefficient of 0.99 and 0.98, respectively. The thermodynamic results showed that the adsorption process is endothermic and spontaneous. After 5 consecutive adsorption-resorption cycles for 2,4-Dichlorophenoxyacetic acid and glyphosate, the removal efficiency was 72 % and 65 %, respectively. SH-magMCM-41 nano-adsorbent can be an effective adsorbent for the removal of 2,4-Dichlorophenoxyacetic acid and glyphosate herbicides.