In the process test of indium column evaporation of infrared detector, sometimes it is necessary to measure a large amount of indium column heights, so the measurement method of indium column height is studied in this paper. The manual method which measures point by point can get accurate results. But the measurement speed is slow and it takes a lot of time.The rapid automatic measurement method uses the scanning function of the microscope and the image recognition technology to automatically identify the indium columns. It can obtain the heights of all indium columns at one time, so the measurement speed is very fast.The steps, procedures and key option settings of the two methods are introduced in detail in this paper.It is estimated that the second rapid measurement method only takes 30 minutes to measure the heights of 1000 indium columns, reducing the measurement time by 76% and greatly improving the measurement efficiency.Finally, the advantages and disadvantages of the two different measurement methods are analyzed.