Quinoa （Chenopodium quinoa Willd.） has rich nutritional and strong stress resistance. In this study， two kinds of quinoa germplasm materials， M059 （fast radicule growth） and M024 （slow radicule growth）， were used to simulate drought stress with PEG-6000. The anatomical structure of seed phenotypes was observed， glucose contents were determined in germinated seeds， and transcripome sequencing was performed on materials treated with normal water and drought. The results of seed phenotype and glucose contents determination showed that the radicles length of M059 and M024 decreased by 68.65% and 71.43%， respectively， after 15% PEG-6000 treatment for 24 h compared with normal water treatment. Under normal water treatment conditions， the contents of total soluble sugar， sucrose， glucose and fructose in M059 were 18.58%， 97.84%， 70.54% and 32.77% higher than those in M024. After being treated with 15% PEG-6000 for 24 h， the sucrose content of M024 was 23.01% higher than that of M059， and the soluble total sugar and glucose content of M059 were 7.26% and 25.00% higher than that of M024， respectively. Venn diagram analysis showed that there were 211 differentially expressed genes in C1vsD1， C2vsD2， C1vsC2 and D1vsD2 comparison groups， and 132， 1270， 578 and 914 differentially expressed genes， respectively. GO and KEGG enrichment analyses showed that 5 GO terms and 3 metabolic pathways were closely related to the molecular response of glucose metabolism in quinoa seeds under drought stress. Based on functional annotations of differentially expressed genes， there were 10 differentially expressed genes （LOC110702784_AGAL2， LOC110719866_INV1， LOC110717843_TPPJ， LOC29490_CELB， LOC110719843_bg1x， LOC110689796_SUS1， LOC110690728_MAN6， LOC110729879_HK2， LOC110712726_EGLC， LOC110734349_FK7） were related to glucose metabolism， and the qRT-PCR verification results of these 10 differentially expressed genes were consistent with the transcriptomic results. The results of this study will provide reference for further analysis of the molecular regulatory mechanism under drought stress in quinoa.