arcpy程序最好不要依赖于arcmap运行程序MakeFeatureLayer_management，而要用CopyFeatures_management

   #执行相交
   pixelPolygonShp = arcpy.MakeFeatureLayer_management(pixelPolygon, "pixelPolygonShp")
   #加载进源shp，判断是否相交
   SourceShp = arcpy.MakeFeatureLayer_management(shp, "SourceShp")
   # 使用Intersect_analysis对两个要素集合对象求交
   intersect_fc = arcpy.Intersect_analysis([pixelPolygonShp, SourceShp], "intersect_fc")

arcpy程序最好不要MakeFeatureLayer_management，这样会在arcmap中产生图层layer，再去调用类似相交分析的功能时，就会在gis中执行，减慢运行速率。

可以选择使用CopyFeatures_management函数先将生成的文件保存到本地，然后在执行其他函数时，函数输入参数不要写为arcmap里现有的图层，而是指定为已经在本地的文件的绝对路径，这样就不会在gis中执行函数，大大提高了运行速率。

 pixelPolygon = arcpy.Polygon(array).projectAs(spatial_ref)
 array.removeAll()
 #保存到本地
 pixelPolygon_shp = os.path.join(rootDir, "pixelPolygon.shp")
 arcpy.CopyFeatures_management(pixelPolygon, pixelPolygon_shp)
 shp = ...（..绝对路径\\*.shp）
 intersect_fc = arcpy.Intersect_analysis([pixelPolygon_shp, shp], intersect_fc)