How do I change variable in a function from another file?

The main answer is that you can't do it exactly as you asked. A variable defined as you have a in app.js is private to the scope of a and only other code within app.js can modify it.

There are a number of other ways you can structure things such that module B can modify something in module A or cause something to be modified in module A.

Global

You can make a global. This is not recommended for a variety of reasons. But you could make it a property of the global object by changing your declaration of a to:

global.a = 1;

Then, in module B, you can directly set:

global.a = 2;

Pass and Return

You can pass a into a function in module B and have that function return a new value that you assign back into a.

const b = require('moduleB');

let a = 1;
a = b.someFunction(a);
console.log(a);    // 2

Then, inside of moduleB, you can modify propertys on a directly:

// inside of moduleB
module.exports.someFunction = function(a) {
    return ++a;
};

Put value in object and pass reference to object

Rather than storing the value in a simple variable, you can store it as a property of an object an you can then pass a reference to that object. Objects in Javascript are passed by ptr so some other function you pass the object to can modify its properties directly.

const b = require('moduleB');

let a = {someProperty: 1};

b.someFunction(a);
console.log(a.someProperty);    // 2

Then, inside of moduleB, you can modify propertys on a directly:

// inside of moduleB
module.exports.someFunction = function(obj) {
    obj.someProperty = 2;
};

First way is return in your change function in second.js.

app.js:

var r=require("./second.js");
var a=1;
a = r.change(a);
console.log(a);

second.js:

module.exports.change=function(a){
    a=2;
    return a;
}

Second way is use object as parameter to pass it by reference:

app.js:

var r=require("./second.js");
var obj={a:1};
r.change(obj);
console.log(obj.a);

second.js:

module.exports.change=function(obj){
    obj.a=2;
}

You can use localStorage or sessionStorage for setting and getting your variable. for node js you can use https://www.npmjs.com/package/localStorage package

//You can set using localStorage.setItem('key','value')

var r = require("./second.js");
var a = 1;
localStorage.setItem('a', 1) /*Window api for setting variable locally 
localStorage.setItem('key','value')*/
r.second(a);
console.log(a);

You can get using localStorage.getItem('key')

//second.js
module.exports.change=function(a){
a=localStorage.getItem('a')
}