Guess you missed the part where they told her that the emperor and her uncle will be gone for a while in war. She obviously developed feelings for her father - the emperor and cares for him deeply. She does not want him to go and possibly get killed. It is a normal feeling for a child to cry when their loved ones leave.
ch 71 P.S.
Fantasy · amarag2020
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Webnovel 
Guess you missed the part where they told her that the emperor and her uncle will be gone for a while in war. She obviously developed feelings for her father - the emperor and cares for him deeply. She does not want him to go and possibly get killed. It is a normal feeling for a child to cry when their loved ones leave.
ch 71 P.S.
Trapped in a Fantasy World
Fantasy · amarag2020