To enhance the understanding of minute-scale precipitation variations in Shandong and improve the forecasting of short-duration heavy rainfall and meteorological disaster warnings, this study analyzed the spatio-temporal distribution and variation characteristics of minute-scale precipitation and short-duration heavy rainfall (1, 5, 10, 20, 30, and 60 minutes) during the flood season (June to September) from 2004 to 2024, based on minute-level precipitation observation data from 122 stations in Shandong. The results indicated that the average minute-scale precipitation frequency during the flood season exhibited a distinct spatial pattern of higher values in the southeast and lower values in the northwest. The average minute-scale precipitation amount was relatively high in areas such as Zaozhuang, southern Linyi, eastern Jining, northern Dezhou, and western Binzhou. Overall, the minute-scale precipitation frequency showed a fluctuating decreasing trend year by year, while the minute-scale precipitation amount demonstrated a significant increasing trend. Precipitation in Shandong primarily occurred in July and August. The period from 01:00 to 08:00 Local Standard Time (LST) was associated with higher frequencies of minute-scale precipitation, whereas the period from 13:00 LST to 01:00 LST the next day was characterized by larger minute-scale precipitation amounts. The most pronounced increases in minute-scale precipitation frequency were observed in parts of northwestern Shandong, northern Weifang, and regions of Linyi, Rizhao, Qingdao, and Yantai. The most significant increases in minute-scale precipitation amount occurred in western Liaocheng, western Zaozhuang and Linyi, Binzhou, Dongying, and central-western Weifang. The maximum precipitation for short durations of 1–60 minutes was highest in areas including Liaocheng, Jinan, Binzhou, northwestern Weifang, southern Zaozhuang and Linyi, southern Qingdao, and western and southern Yantai. The increasing trend in maximum precipitation across various durations was most evident in Weifang, northern Rizhao, northern Binzhou, and Dongying. The multi-year average maximum precipitation for all durations was highest in southern Linyi, central Jining and Tai'an, southwestern Jinan, and northern Dezhou and western Binzhou. The spatial distribution of areas with high relative thresholds for heavy rainfall across various durations was similar to that of the average minute-scale precipitation amount. The relative threshold standards for short-duration heavy rainfall of 1–60 minutes in Shandong were 1.1 mm, 3.5 mm, 5.7 mm, 9.3 mm, 12.3 mm, and 19.3 mm, respectively.