currentTimeMills
/**
* Returns the current time in milliseconds. Note that
* while the unit of time of the return value is a millisecond,
* the granularity of the value depends on the underlying
* operating system and may be larger. For example, many
* operating systems measure time in units of tens of
* milliseconds.
*
* <p> See the description of the class <code>Date</code> for
* a discussion of slight discrepancies that may arise between
* "computer time" and coordinated universal time (UTC).
*
* @return the difference, measured in milliseconds, between
* the current time and midnight, January 1, 1970 UTC.
* @see java.util.Date
*/
public static native long currentTimeMillis();
System.nanoTime
为什么需要
平时产生随机数时我们经常拿时间做种子，比如用 System.currentTimeMillis 的结果，但是在执行一些循环中使用了System.currentTimeMillis，那么每次的结果将会差别很小，甚至一样，因为现代的计算机运行速度很快。
后来看到java中产生随机数函数以及线程池中的一些函数使用的都是 System.nanoTime。
方法声明
/**
* Returns the current value of the running Java Virtual Machine's
* high-resolution time source, in nanoseconds.
*
* <p>This method can only be used to measure elapsed time and is
* not related to any other notion of system or wall-clock time.
* The value returned represents nanoseconds since some fixed but
* arbitrary <i>origin</i> time (perhaps in the future, so values
* may be negative). The same origin is used by all invocations of
* this method in an instance of a Java virtual machine; other
* virtual machine instances are likely to use a different origin.
*
* <p>This method provides nanosecond precision, but not necessarily
* nanosecond resolution (that is, how frequently the value changes)
* - no guarantees are made except that the resolution is at least as
* good as that of {@link #currentTimeMillis()}.
*
* <p>Differences in successive calls that span greater than
* approximately 292 years (2<sup>63</sup> nanoseconds) will not
* correctly compute elapsed time due to numerical overflow.
*
* <p>The values returned by this method become meaningful only when
* the difference between two such values, obtained within the same
* instance of a Java virtual machine, is computed.
*
* <p> For example, to measure how long some code takes to execute:
* <pre> {@code
* long startTime = System.nanoTime();
* // ... the code being measured ...
* long estimatedTime = System.nanoTime() - startTime;}</pre>
*
* <p>To compare two nanoTime values
* <pre> {@code
* long t0 = System.nanoTime();
* ...
* long t1 = System.nanoTime();}</pre>
*
* one should use {@code t1 - t0 < 0}, not {@code t1 < t0},
* because of the possibility of numerical overflow.
*
* @return the current value of the running Java Virtual Machine's
* high-resolution time source, in nanoseconds
* @since 1.5
*/
public static native long nanoTime();
使用方式
比如如下使用：
public static void main(String[] args) {
long start = System.nanoTime();
//do sth...
long end = System.nanoTime();
System.out.println("Time: " + (end - start));
}
使用注意
To compare two nanoTime values
* <pre> {@code
* long t0 = System.nanoTime();
* ...
* long t1 = System.nanoTime();}</pre>
*
* one should use {@code t1 - t0 < 0}, not {@code t1 < t0},
* because of the possibility of numerical overflow.
JDK表明比较两个nanoTime的时候，应该用t1 - t2 > 0的方式来比较，而不能用 t1 > t2的方式来比较，因为nanoTime在获取时有数值溢出的可能。
问什么要这么比较
Nano时间不是’真实’时间，它只是一个计数器，当某些未指定的事件发生时（可能是计算机启动），计数器从一些未指定的数字开始递增。 它会溢出，在某些时候变为负数。 如果你的t0恰好在它溢出之前（即非常大的正数），并且你的t1刚好在（非常大的负数）之后，
则 t1 < t0（即你的条件错误，因为t1发生在t0之后）…..
但是，如果你说 t1-t0 < 0，那么神奇的是，对于相同的溢出（undeflow）原因（非常大的负数减去一个非常大的正数），结果将是t1的纳秒数在t0之后……并且是对的。
在这种情况下，两个错误确实是正确的！
总结
二者的关系
都可以用来计算耗时。
两个方法都不能保证完全精确,精确程度依赖具体的环境.
二者的区别
（1）System.currentTimeMillis 返回的毫秒，这个毫秒其实就是自1970年1月1日0时起的毫秒数.
（2）java 中 System.nanoTime() 返回的是纳秒，nanoTime 而返回的可能是任意时间，甚至可能是负数
时间单位
ns（nanosecond）：纳秒， 时间单位。一秒的 10 亿分之一，即等于10的负9次方秒。常用作 内存读写速度的单位。
1纳秒=0.000001 毫秒
1纳秒=0.00000 0001 秒
拓展阅读
参考资料
java-system-nanotime-runs-too-slow
