This study consists of two parts, model buildingand application. In the first part a model using datafrom different regions and the whole province ofYunnan, China, at county level has been presented toshow the relationship between malaria incidence rate,malaria control activities, environmental and socialeconomic factors. The results show that preventivemedicine and mosquito control activities have negativeeffects on malaria transmission. Other factors such asrainfall, temperature, mobile populations andproportion of farmer population can also affect malariaincidence rate, they have positive effect on malariatransmission. The proxy of variable GCP per capita maynot be good in this model, or it has no effect onmalaria incidence rate. The model cannot reflect theeffect of surveillance and anti-relapse therapyactivities using data from four regions and wholeprovince. Based on the coefficients of determinants ofpreventive medicine and mosquito control activities inthe models and the incidence rate, the marginal effectin four regions was calculated. After analysis ofallocative efficiency and equity, we can get directionas to where and into which activity to input moreresources. The result of allocative efficiency analysisshowed that if there are more resources they should beinvested in mosquito control activities. The results ofallocative equity analysis show that in the south eastand south west region more resources are needed.