add_filter('woocommerce_package_rates', 'hide_shipping_method_based_on_total', 10, 2);
function hide_shipping_method_based_on_total($rates, $package) {
    if (WC()->cart->subtotal < 50) { // Change 50 to your desired threshold
        unset($rates['flat_rate']); // Replace 'flat_rate' with your shipping method ID
    }
    return $rates;
}