Genotyping-by-sequencing (GBS) technology has a capacity for delivering large numbers of single nucleotide polymorphism (SNP) marker genotypes with potentially lower cost than SNP chips. To achieve stable genotyping results, we selected the EcoRI-MspI enzyme from a large number of candidate enzymes, and used the magnet beads-based purification method to stably and simply recapture GBS tags. Genomic DNA samples from 192 Duroc pigs were digested with EcoRI-MspI enzyme, ligated to adapters containing unique barcode, and sequenced on the Illumina NextSeq 500 system with 75bp single-end sequencing. The results showed that all 192 barcoded DNA samples were represented evenly, and that on average 4 million reads per animal were produced. From these samples, about 450,000 unique sequence tags per sample containing 55,843 SNPs were identified through TASSEL4.0 analysis package requiring a minimum of 10 times that a tag must be present, which covered about 1% of the whole genome. The average call rate per individual was more than 94.6%. By repeating GBS genotyping on 2 different samples with 96 pigs in each sample performed by different technicians, 88.5% of the 55,843 SNPs had the same genomic locations from both samples. The cost of the 55,843 SNPs per sample was under $50 per animal. These results showed that our improved GBS technique is sufficiently high-throughput, economical and provides an acceptable marker density for genomic selection or genome-wide association studies.