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I want to run Arduino Mega 2560 outdoor for long time. I found this choices:

1 - 12 V power jack: It makes the board so hot so I skip it.

2 - Vin: It makes the board so hot so I skip it too.

3- 5 V pin: It worked. I heard it makes Arduino unstable because it bypasses the regulator inside it.

How can I solve this? Will 5 V pin work good?

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5V pin will work good yes. this powers the MCU directly and without issues.

Regarding the issue of the "Regulator bypass",this may be a problem because you put 5V in the output of the Regulator (instead of its input).

IF the circuit is designed correctly, the regulator should have a diode (D1), which directs the 5V that you put in its output, to its input like this:

schematic

simulate this circuit – Schematic created using CircuitLab

Even if the diode is not there, It should not make the Arduino unstable.

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    \$\begingroup\$ It could be unstable if the voltage you give it is unstable. \$\endgroup\$ Commented Jun 26, 2021 at 6:39

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