In this article, a modified paper separation channel SERS substrate was fabricated by a pen writing method for the simultaneous separation and detection of thiuram and dimethoate. The hydrophilic channel was fabricated with both sides of hydrophobic barrier by the Alkylketene dimer (AKD) modified paper substrate, of which the flow dynamic was well conformed to the Lucas-Washburn model and could be used to separate pesticides effectively. As modified by Ag nanoparticles (AgNPs) and ZnO nanoparticles (ZnONPs), the hydrophilic channel exhibited high recyclable SERS detection activity and stability. The separation and detection performance with different target proportion, channel width and sample volume were studied in detail, which have significant influence on the diffusion process. Additionally, the Raman detects intensity on the substrate also showed linear relationship from 100 to 1000μg/L. The calculated limit of detects (LODs) under optimal experimental conditions were 54.57 and 19.16μg/L for dimethoate and thiuram, respectively. Due to the loading of ZnONPs, the substrate could be used repeatably with good stability. The convenient preparation, effective separation and repeatability make this paper based separation channel SERS substrate have great potential application on the fast separation and simultaneous detection of various pesticides in complex field.