Onscroll selected checkbox getting unchecked using listiview

Problem is in your getView() method. You set OnCheckedChangeListener and after that you set checkbox to true or false which fires callback in that listener. You should set checkbox check state first and after that set OnCheckedChangeListener.

Also, that boolean checked[] field is useless, so I simplified your code a little:

 public class CustomAdapter extends BaseAdapter {
    private final LayoutInflater inflater;
    private final Context context;
    private List<ModelPooja> listData;

    public CustomAdapter(Context mainActivity, List<ModelPooja> listData) {
        context = mainActivity;
        this.listData = listData;
        inflater = (LayoutInflater) context.getSystemService(Context.LAYOUT_INFLATER_SERVICE);
    }

    @Override
    public int getCount() {
        return listData.size();
    }

    @Override
    public Object getItem(int position) {
        return listData.get(position);
    }

    @Override
    public long getItemId(int position) {
        return 0;
    }

    @Override
    public View getView(final int position, View convertView, ViewGroup parent) {
        final ViewHolder holder;

        if (convertView == null) {
            holder = new ViewHolder();
            convertView = inflater.inflate(R.layout.list_item_poojaselection, null);
            holder.tv = (TextView) convertView.findViewById(R.id.list_item_poojaname);
            holder.checks = (CheckBox) convertView.findViewById(R.id.list_item_poojacheck);
            convertView.setTag(holder);
        }else {
            holder = (ViewHolder) convertView.getTag();
        }
        holder.checks.setOnCheckedChangeListener(null);
        holder.checks.setFocusable(false);

        if (listData.get(position).isselected) {
            holder.checks.setChecked(true);
        } else {
            holder.checks.setChecked(false);
        }

        holder.checks.setOnCheckedChangeListener(new CompoundButton.OnCheckedChangeListener() {
            @Override
            public void onCheckedChanged(CompoundButton cb, boolean b) {

                if (checkMaxLimit()) {

                    if (listData.get(position).isselected && b) {
                        holder.checks.setChecked(false);
                        listData.get(position).isselected = false;

                    } else {
                        holder.checks.setChecked(false);
                        listData.get(position).isselected = false;
                        Toast.makeText(context, "Max limit reached", Toast.LENGTH_SHORT).show();
                    }
                } else {
                    if (b) {
                        listData.get(position).isselected = true;
                    } else {
                        listData.get(position).isselected = false;
                    }
                }
            }
        });

        holder.tv.setText(listData.get(position).getPOOJA_LISTING_NAME());
        return convertView;
    }

    public boolean checkMaxLimit() {
        int countermax = 0;
        for(ModelPooja item : listData){
            if(item.isselected){
                countermax++;
            }
        }
        return countermax >= 5;
    }

    public class ViewHolder {
        TextView tv;
        public CheckBox checks;
    }
}