Rural children are seriously afflicted with intestinal helminth infections in China. Of note, the term rural children includes rural left-behind children (LBC) and rural non-left-behind children (NLBC); the difference in the prevalence of intestinal helminths between the 2 groups remains unclear. In this study, Gulin and Xuyong counties in southern Sichuan were chosen for investigation in 2019. The Kato Katz thick smear method was used to detect the presence of intestinal helminth eggs in rural children. For children aged 3–6 yr, the adhesive tape perianal swab method was used to detect Enterobius vermicularis and tapeworm eggs. Statistical differences in infection rates between the 2 groups were determined by the chi-square test. In total, 1,608 rural children, 911 LBC and 697 NLBC, participated in the investigation. Six species of intestinal helminths were detected. A total of 358 (39.3%) and 130 (18.7%) intestinal helminth positives were found among LBC and NLBC, respectively; the former had a higher (P < 0.05) infection level. Moreover, an analysis of double worm infection rates among intestinal helminth positive LBC and NLBC showed a difference between the 2 groups that was also statistically significant. These surveys indicated that the risk of intestinal helminth infection was substantially higher and the severity of infection much worse in rural LBC in southern Sichuan. More attention should be paid to the parasitic infection of LBC.