Agree with @Teleporting Goat - "came" is correct here. "Had come" is the past perfect tense, which is used to describe something that happened before another action. It would be correct to say, "My boss came to my desk, but my coworker had come already." This means that your coworker was there before your boss. The reason why I think "had come" is incorrect is because you aren't saying that something else happened before your boss came to your desk.
According to me using Had come gives idea about fist completed action of coming to my desk and then second action of explanation.
Close, but "had come" doesn't imply this - at least, not in the original sentence. Your original sentence (with the correct verb) already makes that implication, actually; you don't need "had come" to convey that.
"My boss came to my desk and it took me 10 minutes to explain X to him."
"And" loosely implies a sequence, especially because coming to your desk seems like something that would happen before the explanation.
Some other examples:
"The player kicked the ball and scored a goal."
"I buckled my seatbelt and turned on the ignition."
Both of those sentences are technically correct regardless of the order in which the actions happened. But the implication is that the two actions happened in sequence.