The search for efficient and selective routes for the disassembly of C-lignin and G/S lignin coexisting in Euphorbiaceae seed coats is of great interest and importance, because a plentiful supply of C-lignin can serve as a green carbon feedstock for the production of catechols in a selective manner. Herein, we investigated a series of pretreatment methods for the disassembly of C and G/S lignins in Jatropha seed coats, and extraction by dilute HCl in dioxane was established as the optimized process. This protocol enabled the almost complete segregation of the two types of lignins in Jatropha seeds, and can be generalized to other Euphorbiaceae plants (candlenut, tung, and castor) containing both C and G/S lignins. Characterization by NMR spectroscopic analyses revealed that the isolated lignin samples were mostly composed of benzodioxane units. The disassembled C-lignin samples can produce a single catechylpropanol product (selectivity up to 97%) through Pd/C-catalyzed hydrogenolysis, and are superior to the feedstocks containing C and G/S lignins in terms of catalytic activity and selectivity.