No. Company X has separate legal entity different from that of its managing director or its director. In this situation, company X holds only 1/3 i.e 33.33% of company Y's shares.
As per section 4 of the companies act, more than half of the nominal value of company's equity share capital has to be held by another company (in this case X) to be classified as a subsidiary of that company. So Y would normally not be X's subsidiary.
However, if company X has the power to control the composition of the Board of directors of company Y, then Y will become X's subsidiary, since this is also provided for by sec 4.