This paper builds a selection model of farmers’ behavior of application of pesticides and uses 635 panel data of samples of households from two main apple planting areas of loess plateau and area around the Bohai gulf for estimation. It describes the laws in farmers’ behavior of application of pesticides and its determinants from two dimensions, namely the application of high toxic pesticides and the pesticides input. Research reveals a significant regional difference in farmers’ behavior of application of pesticides, with the application of high toxic pesticides and pesticide input levels in the area around the Bohai gulf higher than those in the loess plateau region in average; and the mechanism of decision-making and determinants vary in two regions too. It further shows that the low cost of high toxic pesticides highly explains farmers’ behavior in abandoning the green pesticides. It is proposed that the government should enhance the rules and regulations for food safety, induce farmers to apply pesticides normally, elevate the construction of industrial organizations, facilitate the innovations in green pesticide technology, perfect the construction of market mechanism, strengthen education to popularize new agricultural technology among farmers. 