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Background : Climate has been considered as influential factor related to Malaria cases in several previous research. However there was still contradiction results in several countries. It is also interesting to find out the effect of intervention methods to Malaria since information about these variables are still limited. Purpose The aims of this research was to analyse the effect of climate and intervention method using model prediction. Methods : This research was analytic study with time series analysis in Menoreh ecosystem, Central Java, Indonesia. Several variables were collected such as temperature, rainfall, intervention methods (the use of mosquito nets, Indoor Residual Spraying, Mass Blodd Survey and number of Malaria cases. Data was collected during 2005-2015 (10 years). Data analysed by poisson regression to assess correlation between variables, and quasi poisson and negative binomial to determine the best model. Results : Result of this study showed that Malaria incidences were influenced by case finding through mass blood survey, and the number of malaria cases in previous month. While climate variables such as temperature and rainfall had no significant correlation with malaria incidence. Conclusion This modelling framework revealed that mass blood survey and the number of malaria cases influenced the malaria incidence. Indeed, it is important to conduct routine mass blood survey and active surveillance to monitor and predict the Malaria cases. Keywords : Climate, Malaria, Mass blood survey