In this study, 149 pairs of InDel primers were used to analyze the genetic diversity of 473 inbred lines of a primary core collection in cucumber. Three methods with twelve sampling proportions were applied to sample the candidate genetic diversity fixed core collections (GDFCC). Number of alleles (Na), number of effective alleles (Ne), Shannon’s information index (I), Gene Diversity, polymorphism information content (PIC), total number of loci and retention rate of loci were used to test diversity and representativeness of the candidate GDFCCs. The results indicated that the method of stepwise clustering plus rare genes preferred sampling with 15% sampling proportion was more efficient for the GDFCC construction. By comparison, Ne, I, Gene Diversity and PIC of the GDFCC were higher than those of the primary core collection, and the retention rate of loci in the GDFCC reached 99.68%. The materials of the GDFCC comes widely from eighteen provinces in China and fifteen foreign countries with a rich diversity and representation. This study provides with a valuable population with genetic stability and extensive representativeness for promoting efficient research and utilization of cucumber germplasm resources.