In situ spacing-correcting heat pulse sensor for measuring sap flow or water flux includes: a holder; a temperature probe or two (sometimes there will be more than two) mounted on the holder; and a heating probe mounted on the holder; wherein two or three thermometric elements are provided axially in the same temperature probe, all the thermometric elements are connected to a data collector, a heating wire is mounted in the heating probe, and the heating wire is connected to a power supply. A measuring method thereof is also provided. In practice, by arranging at least two thermometric elements in each temperature probe, measurement errors of sap flow in plant or soil water flux caused by factors such as deflection of the temperature probe or the heating probe are reduced. Furthermore, the sensor is simple in structure, low in cost, convenient in utilization, and accurate in measurement.