By breaking up soil, tillage often disrupts mycorrhizal extraradical mycelium (ERM). In a core having four windows covered with 37-μm mesh in a perspex box, trifoliate orange (Poncirus trifoliata) seedlings were colonized with an arbuscular mycorrhizal (AM) fungus, Funneliformis mosseae. The core was rotated weekly at 180° around vertical axes, in order to simulate ERM disruption. After 13 such rotations, root mycorrhizal colonization, soil hyphal length inside and outside the core, and plant biomass were substantially reduced. On the other hand, mycorrhizal inoculation without disruption of ERM (static core) was associated with significant increase in biomass production, compared with disruption of ERM (rotating core). Disruption of ERM (rotating core) inhibited the production of easily-extractable glomalin-related soil protein (EE-GRSP) and total GRSP (T-GRSP) inside the core under mycorrhization, due to breakdown of ERM. Mycorrhization markedly increased soil organic carbon content, distribution of water-stable aggregate (WSA) at 0.5–4mm size and mean weight diameter (MWD), whereas core rotation showed a negative effect on MWD and the percentage of WSA within 1–4mm size under mycorrhization and within 0.25–2mm size under non-mycorrhization. It was proposed that soil tillage, in terms of the core rotation, strongly disrupted ERM network, which adversely influenced EE-GRSP and T-GRSP production and plant growth under mycorrhization, subsequently weakening the GRSP functioning on WSA stability.