Advance payment received from my customer in respect of works contract

You have to pay GST advance tax becouse on services advance tax is liability to pay.

You have to issue advance receipt voucher to customer and charge gst on amount received.

Work contract is considered as supply of services and for Services GST is applicable on advances received for Supply of service...You have to issue receipt voucher to Customer.
You have to mention that advance in your GST Return and requires to pay GST on same..

Note : Amount of Advance received is considered inclusive of GST