My boss says, he is so sorry that I do not get too much bonus.
Sounds like your boss values your skillset and appreciates that you stayed onboard during your family struggles.
However, I am actually happy that I am not get fired.
Aren't we all?
What should I answer him?
Concentrate on the positive, period.
Thank you, I am content with the bonus and above all very thankful for being able to work at a such a great place. I sincerely appreciate your understanding with my recent family issues and look forward to what's ahead.
The honest answer would be this: "That I could keep both my family and my job, it makes me actually more happy than a huge bonus in ordinary circumstances!" This is the truth, but it sounds for me somehow... unprofessional.
This sounds like excessive gratitude and can end up putting your boss in a weird position in which they now feel like your savior. It will make them feel like you think they're the sole reason that you're not fired.
Don't make it awkward, he's just doing his job of balancing employee needs. Don't make this some over-the-top dog & pony show.