Q:

after ajax call jquery function's not working

For example :  
$(document.body).on("click", ".main_category", function(){  
    var cat_id = $(this).attr("id");
    $.get("/?category_filter", { cat_id: cat_id }, function(data) {
        $(".owl-wrapper").html(data);
    });
});

$('#conn').isotope({
    // options
    itemSelector : '.owl-item',
    layoutMode : 'fitRows'
});

A:

Try this...
$(document.body).on("click", ".main_category", function(){  
    var cat_id = $(this).attr("id");
    $.get("/?category_filter", { cat_id: cat_id }, function(data) {
        $(".owl-wrapper").html(data);
        $("#conn").isotope("reloadItems").isotope();
    });
});

It will make isotope refresh/rebuild itself after you change the items.