<p>For my server app, I need to check if an ip address is in our blacklist. </p>

<p>What is the most efficient way of comparing ip addresses? Would converting the IP address to integer and comparing them efficient?</p>

Depends what language you're using, but an IP address is usually stored as a 32-bit unsigned integer, at least at the network layer, making comparisons quite fast. Even if it's not, unless you're designing a high performance packet switching application it's not likely to be a performance bottleneck. Avoid premature optimization - design your program for testability and scalability and if you have performance problems then you can use a profiler to see where the bottlenecks are.
Edit: to clarify, IPv4 addresses are stored as 32-bit integers, plus a netmask (which is not necessary for IP address comparisons). If you're using the newer and currently more rare IPv6, then the addresses will be 128 bits long.