Paddy soil is the most important arable land resource in China, the acidification of paddy soil not only reduced the crop yields but also increased the risk of environmental risk. Data from the second national soil survey (1979—1985, the first period) and from the paddy soil quality grading survey (2015—2017, the second period) were collected, and were combined with the national soil testing and formula fertilization data from 2005 to 2015. The spatial analysis and the statistical analysis methods were used to analyze the spatio-temporal variation of paddy soil acidification. During the two periods, the spatial layout dynamic changes of paddy soil pH value and the acidification rate of paddy soil with different pH value levels and regions were analyzed, the correlations between nitrogen input, soil physical and chemical properties and acidification rate of paddy soil were discussed. Besides, the correlation between the nitrogen fertilizer surplus amount from 2015 to 2017 and the change of the paddy soil pH value from 2015 to 2017 was further quantified. The results showed that the intensity of soil acid stress on rice in China was increased during the two periods, especially the increase of area from the acid paddy soils (pH value was 5.5~6.5) to the strongly acid paddy soils (pH value was no more than 5.5), mainly distributed in the middle and southern parts of MLYR (middle and lower Yangtze River), and the central and southern parts of SC (Southwest China). From 1979 to 1985, the average pH value of paddy soil was 6.03, and it was dropped by 0.26 in the year from 2015 to 2017. Among them, the NC (Northeast China), the MLYR (middle and lower Yangtze River) and the SC (Southern China) were dropped by 0.34, 0.29 and 0.58 respectively, while the SW (Southwest China) was increased by 0.14. The acidification rate of the paddy soil survey sites during the two periods from high to low was as follows: alkaline paddy soil, neutral paddy soil, acid paddy soil, strongly acid paddy soil. Regionally, the acidification rate of the paddy soil survey sites during the two periods from high to low was as follows: NC, SC, MLYR, and SW. During the two periods, the paddy soil acidification rate was significantly positively correlated with the change of nitrogen input amount and soil bulk density, but was significantly negatively correlated with the change of paddy soil organic matter content and the plough layer thickness. From 2015 to 2017, there was a significant negative correlation between the nitrogen surplus amount and the change of the paddy soil pH value, such that the nitrogen surplus amount was increased with the decrease of paddy soil pH value. Therefore, the paddy soil remediation zones should apply the balanced fertilization with soil testing formula, control amount of nitrogen fertilizer, and promote environmental-friendly organic manure to replace chemical nitrogen fertilizer. Besides, in the remediation zone mainly with alkaline and neutral paddy soils, the technology of straw chopping and return to the paddy field with rotary tillage or moldboard tillage could be applied to decrease the paddy soil acidification rate. In the remediation zone mainly with acid paddy soils, the technology of straw returning could be applied to maintain the paddy soil pH value. In the remediation zone mainly with strongly acid paddy soils, the agricultural calcareous material could be used to raise the paddy soil pH value.