Background: Although malaria decline has been observed in most sub-Saharan African countries, the disease still represents a significant public health burden in Tanzania. There are contradictions on the effect of ownership of at least one mosquito net at household on malaria mortality. This study presents a Bayesian modelling framework for the analysis of the effect of ownership of at least one mosquito net at household on malaria mortality with environmental factors as confounder variables. Methods: The analysis used longitudinal data collected in Rufiji and Ifakara Health Demographic Surveillance System (HDSS) sites for the period of 1999-2011 and 2002-2012, respectively. Bayesian framework modelling approach using integrated nested laplace approximation (INLA) package in R software was used. The space time models were established to assess the effect of ownership of mosquito net on malaria mortality in 58 villages in the study area. Results: The results show that an increase of 10 % in ownership of mosquito nets at village level had an average of 5.2 % decrease inall age malaria deaths (IRR = 0.948, 95 % CI = 0.917, 0.977) in Rufiji HDSS and 12.1 % decrease in all age malaria deaths (IRR = 0.879, 95 % CI = 0.806, 0.959) in Ifakara HDSS. In children under 5 years, results show an average of 5.4 % decrease of malaria deaths (IRR = 0.946, 95 % CI = 0.909, 0.982) in Rufiji HDSS and 10 % decrease of malaria deaths (IRR = 0.899, 95 % CI = 0.816, 0.995) in Ifakara HDSS. Model comparison show that model with spatial and temporal random effects was the best fitting model compared to other models without spatial and temporal, and with spatial-temporal interaction effects. Conclusion: This modelling framework is appropriate and provides useful approaches to understanding the effect of mosquito nets for targeting malaria control intervention. Furthermore, ownership of mosquito nets at household showed a significant impact on malaria mortality.