Interstitial fluid (ISF) is considered an underutilized source of biomarkers for disease diagnosis and monitoring. However, biomacromolecular markers cannot be enriched in ISF due to the restriction of capillary walls, which limits the wide use of ISF in biomarkers analysis. Here, an integrated micro-extracting system (MES) that includes a multimicrochannel microneedles (MMNs) array and a bilayer suction cup is presented. The system coupled with negative pressure (NP) realizes high-efficiency extraction of ISF and in-situ recruitment of biomacromolecular markers in a minimally invasive manner. By high-precision laser microfabrication technology, internal microchannels are created through pyramidal microneedles (MNs), which convey a concentrated, safe NP around the local dermal capillaries to increase their filtration and permeability, realizing the enrichment of biomacromolecular markers in ISF; meanwhile, the excellent mechanical properties of MMNs promise stable outlets for ISF under NP, achieving high-efficiency extraction. More importantly, compared to the lasting damage caused by applying NP directly to the skin surface, skin tissue is well-tolerated to our MES. The biomacromolecular enriching effect is confirmed by fluorescent substances with different molecular weights in vivo and bone turnover markers in osteoporosis mice model. The system broadens the vision of MN-based microdevices for minimally invasive disease diagnosis and prognosis.