Recent global food crisis combined with a series of natural disasters had a significant impact on the availability and affordability of food in Bangladesh, threatening to reverse the progress made in poverty reduction and hunger elimination achieved in the past decade. In this paper, we examine the direct and indirect linkages between agriculture and nutrition in Bangladeshi households, with a focus on rice. We first investigate the factors of rice productivity at plot, household, and village level by estimating an endogenous switching model of yield by season. Next we inspect the relationship between income and nutrition using a partial linear model to control for household characteristics. Finally we are able to simulate how increased rice yields and elevated rice price affect consumption decisions and nutritional status of households. Estimation results indicate that farmers’ decision to use irrigation and yield response are determined by different factors, including input intensification, land ownership, education, and access to assets and infrastructure. Household nutrition intake is influenced by household asset, household head characteristics, and consumption of own production. Simulation results suggest increasing rice yield is an effective way to improve nutrition intake in Bangladesh. Our results highlight the importance of input availability and timeliness to increase rice production and achieve self-sufficiency. Government investment in rural infrastructure and service proves to increase both food supply and nutrient intake. In the long run, food security and nutrition can only be achieved through adoption of modern technology developed by agricultural R&D and extension activities. There is no evidence of negative impact of rice price on nutrient intake, implying that households are able to cope with high food prices through shifting to less balanced diets or through cutting expenditure in other activities like education and health care. At the same time, policies targeting vulnerable groups are needed to address food insecurity and malnutrition.