Systematic studies on the genesis, properties, and distribution of natural nanoparticles (NNPs) in soil remain scarce. This study examined a soil chronosequence of continuous paddy field land use for periods ranging from 0 to 1 000 years to determine how NNPs in soil changed at the early stages of soil genesis in eastern China. Soil samples were collected from coastal reclaimed paddy fields that were cultivated for 0, 50, 100, 300, 700, and 1 000 years. Natural nanoparticles were isolated and characterized along with bulk soil samples (< 2-mm fraction) for selected physical and chemical properties. The NNP content increased with increasing soil cultivation age at 60 g m−2 year−1, which was related to decreasing soil electrical conductivity (172–1 297 µS cm−1) and NNP zeta potentials (from –22 to –36 mV) with increasing soil cultivation age. Changes in several NNP properties, such as pedogenic iron oxide and total organic carbon contents, were consistent with those of the bulk soils across the soil chronosequence. Notably, changes in NNP iron oxide content were obvious and illustrated active chemical weathering, pedogenesis, and potential impacts on the microbial community. Redundancy analysis demonstrated that the soil cultivation age was the most important factor affecting NNP properties, contributing 60.7% of the total variation. Cluster and principal component analysis (PCA) revealed splitting of NNP samples into age groups of 50–300 and 700–1 000 years, indicating rapid evolution of NNP properties, after an initial period of desalinization (approximately 50 years). Overall, this study provides new insights into NNP evolution in soil during pedogenesis and predicting their influences on agriculture and ecological risks over millennial-scale rice cultivation.