The difference in gold nanoparticle (AuNPs) aggregation caused by different mixing orders of AuNPs, 4-mercaptophenylboronic acid (4-MPBA), and hydrogen peroxide (H2O2) has been scarcely reported. We have found that the color change of a ((4-MPBA + AuNPs) + H2O2) mixture caused by H2O2 is more sensitive than that of a ((4-MPBA + H2O2) + AuNPs) mixture. For the former mixture, the color changes obviously with H2O2 concentrations in the range of 0~0.025%. However, for the latter mixture, the corresponding H2O2 concentration is in the range of 0~1.93%. The mechanisms on the color change originating from the aggregation of AuNPs occurring in the two mixtures were investigated in detail. For the ((4-MPBA + H2O2) + AuNPs) mixture, free 4-MPBA is oxidized by H2O2 to form bis(4-hydroxyphenyl) disulfide (BHPD) and peroxoboric acid. However, for the ((4-MPBA+AuNPs) + H2O2) mixture, immobilized 4-MPBA is oxidized by H2O2 to form 4-hydroxythiophenol (4-HTP) and boric acid. The decrease in charge on the surface of AuNPs caused by BHPD, which has alarger steric hindrance, is poorer than that caused by -4-HTP, and this is mainly responsible for the difference in the aggregation of AuNPs in the two mixtures. The formation of boric acid and peroxoboric acid in the reaction between 4-MPBA and H2O2 can alter the pH of the medium, and the effect of the pH change on the aggregation of AuNPs should not be ignored. These findings not only offer a new strategy in colorimetric assays to expand the detection range of hydrogen peroxide concentrations but also assist in deepening the understanding of the aggregation of citrate-capped AuNPs involved in 4-MPBA and H2O2, as well as in developing other probes.