Supramolecular structure of cellulosic materials from microwave treatment were throughly investigated for production of lignin-containing nanocellulose. The results revealed that both the intermolecular and intramolecular hydrogen bonds were altered by microwave irradiation. Cellulose I_β was the main component in microwave treated bamboo (MTB) with smaller interplanar spacing, and the cellulose molecules were loosely connected resulting in a loose structure. Thereafter, MTB was used to produce lignin-containing nanocellulose by using oxalic acid dihydrate (OAD) to test the feasibility on its efficiency. The chemical consumed for the preparation of lignin-containing nanocellulose (LCN) with a comparable yield (68.08–82.33 %) from MTB was merely 1/10 that from conventional cellulosic materials, indicating the supramolecular structural changes of bamboo cellulose induced by microwave treatment provided suitable conditions for the subsequent hydrolysis of OAD to prepare LCN. The LCN was further added into the polyvinyl alcohol (PVA) matrix endowed excellent UV shielding property and thermal stability for the PVA/LCN films. This study was aimed to provide an environmentally friendly method on the production and application of LCN from bamboo by employing microwave treatment from the perspective of supramolecular level.