BACKGROUND: Over recent decades, hand, foot and mouth disease (HFMD) has emerged as a serious public health threat in the Asia-Pacific region because of its high rates of severe complications. Understanding the differences and similarities between mild and severe cases can be helpful in the control of HFMD. In this study, we compared the two types of HFMD cases in their temporal trends. METHODS: We retrieved the daily series of disease counts of mild and severe HFMD cases reported in mainland China in the period of 2009-2014. We applied a quasi-Poisson regression model to decompose each series into the long-term linear trend, periodic variations, and short-term fluctuations, and then we compared each component between two series separately. RESULTS: A total of 11,101,860 clinical HFMD cases together with 115,596 severe cases were included into this analysis. We found a biennial increase of 24.46 % (95 % CI: 22.80-26.14 %) for the baseline of disease incidence of mild cases, whereas a biennial decrease of 8.80 % (95 % CI: 7.26-10.31 %) was seen for that of severe cases. The periodic variations of both two series could be characterized by a mixture of biennial, annual, semi-annual and eight-monthly cycles. However, compared to the mild cases, we found the severe cases vary more widely for the biennial and annual cycle, and started its annual epidemic earlier. We also found the short-term fluctuations between two series were still significantly correlated at the current day with a correlation coefficient of 0.46 (95 % CI: 0.43-0.49). CONCLUSIONS: We found some noticeable differences and also similarities between the daily series of mild and severe HFMD cases at different time scales. Our findings can help us to deepen the understanding of the transmission of different types of HFMD cases, and also provide evidences for the planning of the associated disease control strategies.