In the present work, a high-throughput field sample preparation method was reported for the simultaneous determination of 5-hydroxymethylfurfural and phenolic compounds in honey. Combining a simple and green homogenous liquid–liquid extraction, matrix-induced sugaring-out, with the use of a 96-deepwell plate and multichannel pipette, the proposed method showed its merits in instrument-free and high-throughput preparation. Due to the high-throughput property, the parameters of the method were rapidly and systematically studied using a constructed 4 × 2 × 4 × 3 array (sample amount × ratio of ACN:H2O × standing time × replicates) in a 96-deepwell plate. Analytical performance was fully validated, and the limits of detection and limits of quantification were in the range of 0.17–1.35 μg/g and 0.51–4.14 μg/g, respectively. Recoveries were between 83.98 and 117.11%, and all the precisions were <5%. Furthermore, the developed method was successfully applied in the outdoor preparation of commercial honey samples and the in-field preparation of raw honey samples in apiary. The current work presented a simple, rapid, and high-throughput method for the field sample preparation of honey and provides a valuable strategy for the design of field and on-site sample preparation.