Crop productivity in cold waterlogged paddy fields can be constrained by chronic flooding stress and low temperature. Farmers typically use chemical fertilizer to improve crop production, but this conventional fertilization is not very effective in a cold waterlogged paddy field. Biochar amendment has been proposed as a promising management approach to eliminating these obstacles. However, little is known about the performance of biochar when combined with N fertilizer and P fertilizer in cold waterlogged soils. The aim of this study was, therefore, to assess the main effects and interactive effects of rice straw biochar, N and P fertilizer on rice growth and soil properties in a cold waterlogged paddy field. The field treatments consisted of a factorial combination of two biochar levels (0 and 2.25 t ha−1), two N fertilizer levels (120.0 and 180.0 kg ha−1) and two P fertilizer levels (37.5 and 67.5 kg ha−1) which were arranged in a randomized block design, with three replicates. Results confirmed that biochar application caused a significant increase in the soil pH due to its liming effect, while this application resulted in a significant decrease in soil exchangeable cations, such as exchangeable Ca, Mg, Al and base cations. The interactive effect of N fertilizer, P fertilizer and biochar was significant for soil total N. Moreover, a negative effect of biochar on the internal K use efficiency suggested that K uptake into rice may benefit from biochar application. According to the partial Eta squared values, the combined application of N fertilizer and biochar was as effective as pure P fertilization at increasing straw P uptake. The addition of biochar to farmers’ fertilization practice treatment (180.0 kg N ha−1, 67.5 kg P2O5 ha−1 and 67.5 kg K2O ha−1) significantly increased rice yield, mainly owing to improvements in grains per panicle. However, notable effects of biochar on rice yield and biomass production were not detected. More studies are required to assess the long-term behavior of biochar in a cold waterlogged paddy field. This study may lay a theoretical foundation for blended application of biochar with fertilizer in a cold waterlogged paddy field.