Bt hybrid cotton (Gossypium hirsutum L.) was intercropped in paired row (PR) planting at 90×135×45 cm inVertisols at Central Institute for Cotton Research, Nagpur, India (21°09’N 79° 09’E, altitude 331 MSL) during 2008, 2009 and 2010 years. Paired row planted Bt hybrid cotton was intercropped (45/135 cm) with marigold (Tagetes erecta L)/soybean (Glycine max L.)/hybrid maize (Zea mays L.)/castor (Ricinus communis L.)/field bean (Dolichus lablab L.) + fennel (Foeniculum vulgare Mill. syn. F) compared with sole Bt hybrid cotton and conventional strip cropping of Bt hybrid cotton + pigeon pea (Cajanus cajan L.) in 90×45 cm in 8:2 ratio in Randomised Block Design. Sole Bt hybrid cotton was planted at 90 × 45 cm significantly out yielded over paired row Bt hybrid cotton (135 × 45 cm) only in normal to deficit rainfall years. PR planted Bt hybrid cotton population was insufficient to exploit the resources under adverse climatic conditions and needed more closer spacing than 45 cm. Pigeon pea strip and castor intercropping reduced the biomass, yield, nutrient uptake and recovery of applied fertilizer in Bt hybrid cotton, but better performed in a year of high rainfall. N, P uptake, NPK fertilizers recovery were significantly higher in sole Bt hybrid cotton which was similar to that of PR Bt hybrid cotton based intercropping systems. NUE were not significantly improved in intercropping systems in the absence of sufficient plant populations of both cotton and intercrops under adverse climatic conditions. Paired row Bt hybrid cotton significantly improved fertilizer uptake, recovery and benefitted from N fertilizer applied to intercropped marigold/maize. Bt hybrid cotton intercropped with castor/ field bean and fennel or marigold systems produced similar net returns of 880 to 940 US $ compared to 460 and 640 US $ ha-1 in paired row and sole Bt hybrid cotton respectively. Key words: Bt hybrid cotton, cotton equivalent yield, fertilizer recovery, fertilizer use efficiency, intercropping, nutrient use efficiency, small farms.