A pipe connector structure includes a base, having a through hole and a revealed upper surface, comprising a first thread portion for connecting to an intercommunicating device and a second thread portion located on the first thread portion; a lid, having a central through hole; a sleeve, accommodated in the lid; and a first O-ring, disposed at the revealed upper surface and encircling the through hole. The lid includes an inner thread structure corresponding to a thread of an outer sidewall of the second thread portion. Accordingly, a user is capable of accurately cutting a water cooling pipe having an appropriate length according to the revealed upper surface of the pipe connector structure, thereby effectively solving issues of being uncertain whether the water cooling pipe is completely inserted into the base and being likely inserted in an unaligned manner as well as reducing risks of liquid leakage.