The invention belongs to the technical field of geoscience, and particularly relates to a deep alteration mineral three-dimensional modeling method. The method comprises the following steps: step 1, carrying out hyperspectral scanning on a drilled core image; 2, preprocessing the borehole core imaging hyperspectral data; Step 3, performing rock core alteration mineral mapping; 4, calculating the relative content of the rock core alteration minerals of the unit section; 5, displaying the relative content of the borehole alteration minerals in a three-dimensional mode; 6, carrying out parallel section projection; Step 7, carrying out three-dimensional space vectorization; And step 8, carrying out three-dimensional space interpolation on the alteration minerals. According to the method, the deep alteration mineral three-dimensional solid model is established, the deep drilling rock core alteration mineral extraction result is fine, objective and accurate, the modeling precision is high, and the method has important practical application value for deep geological research and prospecting exploration.