An in-field multi-spectral computer vision system was developed using virtual instrument for capturing crop growth status precisely in real time to supervise a variable rate application. The system used a high resolution multi-spectral camera (MS3100) of acquiring excellent multi-spectral images (near-infrared, red and green) to shoot crop images. Labview and its vision development module were adopted to do image acquisition, processing and analysis programs for measuring the crop reflectance of red, green and near-infrared. The test trail of system shows that it can analyze the crop multi-spectral images and compute the spectral characteristics correctly. The average running time of acquiring and processing images of each group (NIR, R and G) were 311ms in the range of 2.4m×1.8m. The running speed of system can satisfy the in-field on-line job of the variable precision application.