A web transaction system and a controlling method thereof are provided. The controlling method of web transaction system includes the following steps. The translating information of a temporary unit is provided to a first service unit by a web transaction system. Whether the temporary unit has received a first transaction element of the first service unit is determined. The translating information of the first service unit is provided to a second service unit. Whether the first service unit has received a second transaction element is determined. If the first service unit has received the second transaction element and the temporary unit has received the first transaction element, then the first transaction element is sent to the second service unit from the temporary unit.