A multi-level evaluation index system is established with farmland protection as the target layer, farmland quantity, farmland quality and farmland sustainable development as the criterion layer. And the index layer includes the quantity change of farmland, per capita farmland area, multiple cropping index, total grain yield, unit grain yield, per capita grain security coefficient, and unit machinery dynamical input. Both expert evaluation method and factor analysis method are used to determine the weight of index. According to the data in farmland area, grain yield and economic development in Urumqi—Changji Economic Zone in the years 1996-2007, a comprehensive evaluation model of intensive farmland use in Urumqi—Changji Economic Zone is established after data standardization. The overall implementation effect of farmland protection policy is analyzed by integrating the farmland quantity, farmland quality and sustainable development. Result shows that implementation effect of farmland protection shows an upward trend in general in Urumqi—Changji Economic Zone in the years 1996-2007, with a fluctuation in the years 2000-2003 and a stable rising phase from 2004 till now. The maximum value is 0.779 in the year 2007; the minimum value is 0.242 in the year 1996; and the mean value in the years 1996-2007 is 0.454. Farmland protection at first strictly controls the farmland quantity, then pays attention to farmland quality, and finally focuses on the sustainable use of farmland.