To develop green super rice varieties with high and stable yields under the rainfed conditions and improved nutrient use efficiency (NuUE), a modified backcross (BC) breeding approach was adopted using a high yielding and widely adaptable Xian variety, WTR1, as the recipient and a Geng variety, HAN, as the donor. Starting from the BC1F2 generation, the BC population had gone through one generation of selection under the IG, LI and RF conditions, followed by consecutive four generations of screening and selection for high GY under six different nutrient conditions, leading to the development of 230 BC1F6 introgression lines (ILs). The final evaluation of the 230 ILs under the six nutrient conditions identified many ILs with improved yields under various combinations of nutrient deficient conditions, including 12 promising lines that had significantly improved NuUE under two or more nutrient deficiency conditions. Our results demonstrated an efficient inter-subspecific BC breeding procedure with first round selection under the rainfed-drought condition followed by four generations of progeny testing for yield performances under six different nutrient conditions. The promising ILs were studied under replicated yield trials under 75N and -NPK conditions for developing high yield rice varieties with improved NuUE. Our results indicated that NuUE in rice was controlled by complex genetic and physiological mechanisms and the developed ILs provided useful materials for genetic and molecular dissection of NuUE in rice.