A two-step process and a direct alkaline transesterification process in preparation for cogeneration alpha-tocopherol and biodiesel (fatty acid methyl esters, FAME) from cottonseeds were studied in this article. The effects of some factors on recovery of alpha-tocopherol and conversion of cottonseed oil (triacylglycerols, TAGs) to biodiesel in the two processes were systematically studied by single factor experiments and orthogonal design method. In the two-step process, alpha-tocopherol and biodiesel were produced from extraction with two-phase solvent followed by base-catalysed transesterification. Approximately 95.5% TAGs was converted into biodiesel, and 1.008 mg/g (wet basis) alpha-tocopherol was detected on the condition:1:3 petroleum ether/methanol volume rate, 40 degrees C extraction temperature; 7:1 methanol/cottonseed oil molar ratio, 1.1% KOH (w/v) concentration in methanol and 60 degrees C esterification temperature. And in the direct alkaline transesterification reaction, 98.3% conversion of TAGs and 0.986 mg/g content of alpha-tocopherol could be achieved at 60 degrees C in 2 h. Both of the two processes were feasible from the economic point of view for further utilisation of cottonseed.