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I'm using MPU 6050 and there's a thermometer onboard. However, I looked through the chip set data sheets but could not find the instruction for temperature sensing.

Could you tell me how to calibrate the data string from the two address started from 0x41?

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The temperature sensor is likely included to keep the gyroscope and accelerometer better calibrated over the specified temperature range. The temperature may not be the ambient temperature should the chip warm up.

The temperature sensor specifications are in section 6.3 on page 14 of the specification sheet indirectly pointed to in the question.

TEMPERATURE SENSOR 
Range -40 to +85°C
Sensitivity Untrimmed 340 LSB/ºC
Temperature Offset 35ºC -521 LSB
Linearity Best fit straight line (-40°C to +85°C) ±1°C

So, when the chip is at 35C the chip temperature register is supposed to read about -521. To convert that into C you need to make a calculation:

chip_temperature = ((value_read + 521) + (35 * 340)) / 340

Simplified:

chip_temperature = (value_read + 12421) / 340

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