How to get the current time in milliseconds from C in Linux?

This can be achieved using the POSIX clock_gettime function.

In the current version of POSIX, gettimeofday is marked obsolete. This means it may be removed from a future version of the specification. Application writers are encouraged to use the clock_gettime function instead of gettimeofday.

Here is an example of how to use clock_gettime:

#define _POSIX_C_SOURCE 200809L

#include <inttypes.h>
#include <math.h>
#include <stdio.h>
#include <time.h>

void print_current_time_with_ms (void)
{
    long            ms; // Milliseconds
    time_t          s;  // Seconds
    struct timespec spec;

    clock_gettime(CLOCK_REALTIME, &spec);

    s  = spec.tv_sec;
    ms = round(spec.tv_nsec / 1.0e6); // Convert nanoseconds to milliseconds
    if (ms > 999) {
        s++;
        ms = 0;
    }

    printf("Current time: %"PRIdMAX".%03ld seconds since the Epoch\n",
           (intmax_t)s, ms);
}

If your goal is to measure elapsed time, and your system supports the "monotonic clock" option, then you should consider using CLOCK_MONOTONIC instead of CLOCK_REALTIME.

You have to do something like this:

struct timeval  tv;
gettimeofday(&tv, NULL);

double time_in_mill = 
         (tv.tv_sec) * 1000 + (tv.tv_usec) / 1000 ; // convert tv_sec & tv_usec to millisecond

Following is the util function to get current timestamp in milliseconds:

#include <sys/time.h>

long long current_timestamp() {
    struct timeval te; 
    gettimeofday(&te, NULL); // get current time
    long long milliseconds = te.tv_sec*1000LL + te.tv_usec/1000; // calculate milliseconds
    // printf("milliseconds: %lld\n", milliseconds);
    return milliseconds;
}

About timezone:

gettimeofday() support to specify timezone, I use NULL, which ignore the timezone, but you can specify a timezone, if need.

@Update - timezone

Since the long representation of time is not relevant to or effected by timezone itself, so setting tz param of gettimeofday() is not necessary, since it won't make any difference.

And, according to man page of gettimeofday(), the use of the timezone structure is obsolete, thus the tz argument should normally be specified as NULL, for details please check the man page.