Different from previous studies on effect of weathering upon geochemical variation along a single weathered profile, this paper provides a new methodology validated by comparing a weathered outcrop samples and their stratigraphic counterpart un-weathered core samples in a nearby shallow borehole. This outcrop and borehole penetrated the Ordovician-Silurian Wufeng–Longmaxi shales, located in the same anticline structure in the northern part of Guizhou Province, Southern China. The mineral composition, major, trace and rare earth elements (REEs) composition and Rock-Eval parameters of outcrop and core samples were analyzed and compared. Organic matter (OM) was observed in the microscope and extracted for elements analysis. The results show that short-term weathering still has significant influence on OM, mineral and elemental composition of black shales. The elements composition shows the outcrop profile was moderately weathered. The REEs compositions do not alter much during weathering process and the REEs composition and their relative ratios still are valid for rock origin determination. The OM, mainly composed by graptolite and bitumen, even entering the highly-over thermal maturity, is still sensitive to the weathering with a systematic loss 30–50% of TOC along the outcrop profile, which suggests that the OM consumption is predominantly controlled by weathering duration and the distance from the weathering surface. In turn, OM has significant influence on the trace elements transportation behavior during weathering. Some trace elements associated with the OM such as V, Cr, Th, U, Ni and Co, change significantly in their absolute concentration during weathering, but their relative ratios do not necessarily change too much and might be still reliable proxies for paleo-environmental determination. The mobility of shale minerals during weathering is in the following order: plagioclase > potassium feldspar and dolomite >pyrite and OM. Short-term weathering can also result in considerable transportation of elements and significant variation of minerals content in black shale, which may pose potentially high environmental and engineering risk in the regions rich in black shale.