Cryptomeria japonica was treated with 90% pyridinium chloride ([Py]Cl) and 10% water w/w solution at 80 and 120 °C. Most hemicellulose in C. japonica was liquefied and over half the lignin in C. japonica was solubilized after treatments at 80 and 120 °C. However, cellulose was mostly insoluble at 80 °C and partially soluble at 120 °C. The crystal structure of cellulose in the cell walls was retained after treatment at 80 °C for 48 h. The degradation products from the polysaccharides were obtained in different yields. The 90% [Py]Cl and 10% water w/w solution is effective for the treatment of lignocellulosics, such as liquefaction of lignocellulosics and the production of useful low molecular weight compounds.