Ecosystem size and resource flows are key factors driving biodiversity and ecosystem function. However, the question of whether and how these drivers interact has been largely overlooked. Here, we investigated how ecosystem size asymmetry affects biodiversity and function of two-patch meta-ecosystems connected through flows of non-living resources. We conducted a microcosm experiment, mimicking spatial resource flows between ecosystems of different sizes yet otherwise identical properties or between ecosystems of the same size. Meta-ecosystems with asymmetric ecosystem sizes displayed higher α- diversity but lower β-diversity and ecosystem function (total biomass) than their unconnected counterparts. At the same time, such an effect was not found for meta-ecosystems of identical patch sizes. Our work demonstrates how the size of ecosystems, interconnected via resource flows, can modulate cross-ecosystem dynamics, having implications for biodiversity and function across scales.