No, there is no provision under the GST law to allocate part payment of the invoice towards the taxes first so that the input tax credit can be allowed. Second proviso to Section 16(2) of the CGST Act clearly provides that the entire value of supply (with tax) is to be paid within 180 days from the date of issue of invoice. Therefore, as long as the entire payment is made within 180 days, the recipient would be entitled to claim the credit in full.
Assuming that only part payment is made within 180 days, availing of proportionate credit based on such part payment is not provided for under the CGST Act. However, Rule 37 of the CGST Rules, provides for availability of the amount of input tax credit availed of proportionate to such amount paid to the supplier.
(ICAI FAQ PUBLICATION 06-09-2017 INPUT TAX CREDIT: FAQ NO.7)