Silicon (Si) is beneficial for rice health and production by alleviating various biotic and abiotic stresses. However, the continual export of grain off-farm may result in Si deficiency for rice plants. The current levels of plant available Si (PASi) in rice paddies in China remain unclear, as do the factors that control PASi content in these soils. We conducted a nationwide sampling campaign across the paddy fields of China between 2016 and 2019, and used calcium chloride extractable Si (Si-CaCl2) and buffered acetate extractable Si (Si-NaAc, pH = 4) to quantify PASi. We show that Si-CaCl2 pool was mainly influenced by mean annual temperature (MAT), soil salinity, soil organic carbon (SOC), mean annual precipitation (MAP), and soil pH, suggesting both pedological and biological control mechanisms. However, the Si-NaAc pool was influenced most by soil pH, MAT and MAP, implying pedological control. Compared to data from the 1990s, the Si-NaAc content decreased by 14.1% on a national scale with an annual decline rate of 0.54%. Based on our investigation, at least 65% of China’s paddy fields are deficient in PASi, which is an increase in area of ~15% over the last 20 years. The principal regions where PASi deficiency was recorded are mainly located in southern China, with the levels of Si deficiency lowering as the paddy fields are located further north. The continual off-site removal of PASi from rice grain and straw will need to be addressed through the use of Si-fertilizers, including organic amendments, to maintain a productive and sustainable rice industry in China.