Owing to the excessive use of pesticides in greenhouses, soils and vegetables herein are more heavily contaminated than those in non-facility cultivation. Based on a developed QuEChERS (quick, easy, cheap, effective, rugged, and safe) method, four methods of sample pretreatment were compared for the monitoring of six pesticides (bifenthrin, chlorfenapyr, lambda-cyhalothrin, pyridaben, pyrimethanil, and pyriproxyfen) commonly used in greenhouses of Hubei Province. Using different extraction strategies and purification methods with different solid phases and eluent mixtures, an optimised method for residual analysis in soil and plant samples via gas chromatography–mass spectrometry was determined. The detection limits of the method for the six pesticides ranged from 0.1 to 0.8 µg/kg in three spiked matrixes and average recovery rates of 80.6–118.3% were achieved for single target pesticides at spiked concentrations of 0.1, 1.0, and 10 mg/kg with standard deviations of 2.4–8.4%. Health risk assessment was conducted through the analysis of greenhouse soil and vegetable samples at Pengdun, a typical agricultural greenhouse facility in Jingmen, Hubei Province, central China. Based on the quantification of the six target compounds in four vegetable types, only pyriproxyfen in tomato exceeded the Canadian and WHO/FAO maximum residue limits. No chronic, acute, non-carcinogenic, or carcinogenic health risks to farmers working in the greenhouses or consumers of the vegetables were observed for all age groups in the study area. Residual results showed that pyridaben is the most often quantified pesticide in all greenhouses of the study area. Pesticide combinations, including bifenthrin, chlorfenapyr, and pyridaben, were similar for cucumbers and eggplants. Nevertheless, simultaneous detection of multiple contaminants and health risk assessment are required because combined contamination may lead to much higher toxicity to both workers and consumers with the emergence of pesticide resistance and the development of new pesticide products. The quantification limits of the developed method for the simultaneous analysis of the six target pesticides showed high reliability, accuracy, effectiveness, and applicability.