Skin interstitial fluid (ISF) is considered as an emerging source of biomarkers with physiological and medical significance. Microneedle arrays (MNs) provide a promising means for painless, noninvasive detection of these biomarkers. Here, novel MNs integrated with photonic crystal (PhC) barcodes are presented, and multiplex specific detection of ISF biomarkers is realized for the first time. The PhC barcodes‐loaded flexible MNs are simply fabricated by replicating dynamic ferrofluid‐cast micromoldings. When the prepared MNs are inserted into skin, they can enrich specific biomarkers to their probes‐decorated PhC barcodes. Thus, by adding corresponding fluorescent probes to form sandwich immunocomplexes, the relative content of the biomarkers can be read out through the fluorescence intensity of the barcodes; meanwhile, the species of these biomarkers can be clearly distinguished by the reflection peaks of the PhC barcodes. Based on the encoded MNs, their sensitivity, flexibility, and versatility of capturing and detecting three inflammatory cytokines are demonstrated in a sepsis mice model. Compared with existing MNs for ISF detection, the encoded MNs not only possess equivalent detection effects with less post‐processing and simplified procedures, but can also detect multiple biomarkers simultaneously, which makes them ideal in many clinical and biomedical detection areas.