Soil organic matter (SOM) is an essential soil property for assessing the fertility of paddy soils in South China. In this study, a set of micro-tractor-based on-the-go device was developed and integrated to measure in-situ soil visible and near infrared (VIS–NIR) spectroscopy and estimate SOM content. This micro-tractor-based on-the-go device is composed of a micro-tractor with toothed-caterpillar band, a USB2000+ VIS–NIR spectroscopy detector, a self-customized steel plow and a self-customized compact spectroscopy probe with a sapphire windows. Two study area are selected, one is located in Hunan, the other in Jiangxi provinces, P. R. China. In each study area, vis-NIR spectra of 50 sites were collected by on-the-go spectroscopy detector and the corresponding topsoil were collected using a cubic soil sampler (10 cm×10 cm×20 cm). Then soil samples were air dried, ground and sieved to a size fraction of less than 2 mm. SOM was measured using the H2SO4-K2Cr2O7 oxidation method at 180℃ for 5 minutes and VIS–NIR spectra were measured again in the laboratory condition using an USB2000+ linked to a laptop by an USB cable. Based on laboratory spectra, direct standardization (DS) method was applied to remove environmental factors from field spectra. The resulting data were divided into calibration (34 samples) and validation (16 samples) sets in two fields, respectively. A partial least square regression (PLSR) was used to predict SOM using on-the-go spectra, laboratory spectra and DS-transferred spectra. SOM spatial distribution maps developed using the on-the-go measured VIS-NIR spectra and the laboratory measured validation dataset were compared. Being interfered by environmental factors, especially water in the soil, the prediction accuracy of SOM using on-the-go spectra spectra (RPD between 0.9995 and 1.3561) were less than these using laboratory spectra (RPD between 1.7747 and 1.8981). Predictions of SOM with the DS-transferred spectra (RPD between 1.6261 and 1.6671) were more accurate than these with on-the-go spectra. Both of two maps showed partial similarity at most areas over two fields. Research results indicated a great potential to estimate SOM in the field using our on-the-go vis-NIR spectroscopy platform combing DS method.