Wi-Fi Calling, which is used to make and receive calls over the Wi-Fi network, has been widely adopted and deployed to extend the coverage and increase the capacity in weak signal areas by moving traffic from LTE to Wi-Fi networks. However, the security of Wi-Fi Calling mechanism has not been fully analyzed, and Wi-Fi Calling may inherently have greater security risks than conventional LTE calling. To provide secure connections with confidentiality and integrity, Wi-Fi Calling leverages the IETF protocols IKEv2 and IPSec. In this paper, we analyze the security of Wi-Fi Calling specifications and discover several vulnerabilities that allow an adversary to track the location of users and perform DoS attacks. By setting up a rogue access point in live testbed environment, we observe that user devices can leak the International Mobile Subscriber Identity (IMSI), despite it being encrypted. The leaked information can be further exploited for tracking user locations. We also discuss how these protocols are vulnerable to several denial of service attacks. To protect user privacy and services against these attacks, we propose practical countermeasures. We also present trade-off considerations that pose challenges for us to apply countermeasures to mitigate the existing vulnerabilities. Additionally, we propose to introduce corresponding amendments for future specifications of protocols to address these trade-offs.